6VP1

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 = 193.014α = 90
b = 57.684β = 107.39
c = 57.684γ = 90
Symmetry
Space GroupC 1 2 1

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
11.4537.2997.60.0540.0630.0320.998133.6104561
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)
11.451.4797.20.6570.7850.4210.7953.3

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 REPLACEMENTTHROUGHOUT2QCB1.4531.0799005538797.30.17680.17570.1974RANDOM17.8
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]
-0.06-0.030.010.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.715
r_dihedral_angle_4_deg23.771
r_dihedral_angle_3_deg13.229
r_dihedral_angle_1_deg7.88
r_angle_refined_deg3.022
r_angle_other_deg1.792
r_chiral_restr0.094
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.715
r_dihedral_angle_4_deg23.771
r_dihedral_angle_3_deg13.229
r_dihedral_angle_1_deg7.88
r_angle_refined_deg3.022
r_angle_other_deg1.792
r_chiral_restr0.094
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3652
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms160

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing