6VOZ

Artificial Metalloproteins with Dinuclear Iron Centers


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QCB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP42982.0 M ammonium sulfate, 0.1 M sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.3146.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.684α = 90
b = 57.684β = 90
c = 184.193γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.9795SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.337.2999.90.0710.0740.020.99919.213.338785
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3299.21.4471.5090.4210.79212.6

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 REPLACEMENTTHROUGHOUT2QCB1.331.0736637193399.340.18080.17950.2064RANDOM18.697
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]
0.070.07-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.279
r_dihedral_angle_3_deg13.776
r_dihedral_angle_4_deg12.758
r_dihedral_angle_1_deg7.945
r_angle_other_deg3.135
r_angle_refined_deg2.841
r_chiral_restr0.106
r_bond_other_d0.038
r_gen_planes_other0.022
r_bond_refined_d0.018
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.279
r_dihedral_angle_3_deg13.776
r_dihedral_angle_4_deg12.758
r_dihedral_angle_1_deg7.945
r_angle_other_deg3.135
r_angle_refined_deg2.841
r_chiral_restr0.106
r_bond_other_d0.038
r_gen_planes_other0.022
r_bond_refined_d0.018
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms913
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing