3C78
0.98 A crystal structure of nitrophorin 4 from Rhodnius prolixus containing FE(III) 2,4 dimethyl deuteroporphyrin ix complexed with ammonia at ph 7.5
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1X8P | PDB ENTRY 1X8P |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 300 | AMMONIUM PHOSPHATE, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.57 | 20.94 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 69.873 | α = 90 |
| b = 42.49 | β = 94.08 |
| c = 52.633 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | BENT CONICAL SI-MIRROR (RH COATING) | 2005-02-23 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | APS | 14-BM-C | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||
| 1 | 0.98 | 20.28 | 85.5 | 0.08 | 0.08 | 30.3 | 4.52 | 75395 | 13.4 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 0.98 | 1.02 | 72 | 0.4 | 0.4 | 4.3 | 2.04 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | FOURIER SYNTHESIS | FREE R | PDB ENTRY 1X8P | 0.98 | 20.3 | 75355 | 3769 | 85.5 | 0.167 | 0.165 | 0.189 | RANDOM | 13.95 | ||||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| 0.02 | -0.26 | -0.06 | 0.01 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.02 |
| r_dihedral_angle_3_deg | 12.115 |
| r_dihedral_angle_1_deg | 7.06 |
| r_dihedral_angle_4_deg | 6.927 |
| r_sphericity_free | 6.482 |
| r_sphericity_bonded | 3.857 |
| r_scangle_it | 3.637 |
| r_scbond_it | 2.931 |
| r_angle_refined_deg | 2.446 |
| r_mcangle_it | 2.248 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1734 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 278 |
| Heterogen Atoms | 42 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| CrystalClear | data scaling |
