4YL4 | pdb_00004yl4

1.1 Angstrom resolution X-ray Crystallographic Structure of Psudoazurin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BQK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529330% PEG 4000, 0.1 M Tris, 0.1M magnesium chloride, 5% Glycerol
Crystal Properties
Matthews coefficientSolvent content
2.2845.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.019α = 90
b = 63.2β = 90
c = 67.045γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2010-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.15097.10.060.34747290
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.1499.646.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1BQK1.113.0444879238797.10.149510.147580.150.185710.18RANDOM18.775
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]
0.12-0.190.06
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free61.556
r_dihedral_angle_2_deg40.197
r_sphericity_bonded28.171
r_dihedral_angle_3_deg12.882
r_rigid_bond_restr11.099
r_long_range_B_refined8.835
r_dihedral_angle_1_deg6.969
r_dihedral_angle_4_deg6.427
r_scbond_it6.064
r_angle_refined_deg2.418
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms911
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection