5FCK

COMPLEMENT FACTOR D IN COMPLEX WITH COMPOUND 5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FBE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2931 uL FD solution (18 mg/mL FD, 10 mM Tris pH 7.0, 100 mM NaCl) was mixed with 1 uL reservoir solution (25% PEG3350, 100 mM TRIS pH 8.0) and equilibrated against 1 mL reservoir solution.
Crystal Properties
Matthews coefficientSolvent content
1.9537.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.266α = 90
b = 48.742β = 108.82
c = 54.73γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 922011-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54

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
11.8622.8789.80.05911.72.414490
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.9149.80.1941.6

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5FBE1.8622.871376472589.980.189350.186840.2372RANDOM18.035
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]
-0.190.030.130.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.28
r_dihedral_angle_4_deg23.378
r_dihedral_angle_3_deg15.42
r_dihedral_angle_1_deg6.735
r_long_range_B_other4.506
r_long_range_B_refined4.471
r_scangle_other3.303
r_mcangle_other2.205
r_mcangle_it2.203
r_scbond_it2.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.28
r_dihedral_angle_4_deg23.378
r_dihedral_angle_3_deg15.42
r_dihedral_angle_1_deg6.735
r_long_range_B_other4.506
r_long_range_B_refined4.471
r_scangle_other3.303
r_mcangle_other2.205
r_mcangle_it2.203
r_scbond_it2.127
r_scbond_other2.076
r_angle_refined_deg1.914
r_mcbond_it1.521
r_mcbond_other1.51
r_angle_other_deg0.89
r_chiral_restr0.117
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1684
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing