6UIZ

Artificial Iron Proteins: Modelling the Active Sites in Non-Heme Dioxygenases


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429526 mg/mL, 2.0 M ammonium sulfate, 0.1 M sodium acetate pH 4
Crystal Properties
Matthews coefficientSolvent content
2.3247.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.75α = 90
b = 57.75β = 90
c = 184.499γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9795SSRLBL9-2

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
11.8537.3799.90.2230.2340.070.99610.110.913859
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)
11.851.891001.3961.4610.4250.7932.311.3

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 REPLACEMENTTHROUGHOUT2QCB1.8537.371310072299.730.18630.18380.2335RANDOM19.545
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]
-0.21-0.210.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.205
r_dihedral_angle_4_deg19.241
r_dihedral_angle_3_deg15.352
r_dihedral_angle_1_deg8.008
r_angle_other_deg3.305
r_angle_refined_deg2.994
r_chiral_restr0.084
r_bond_other_d0.038
r_gen_planes_other0.023
r_bond_refined_d0.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.205
r_dihedral_angle_4_deg19.241
r_dihedral_angle_3_deg15.352
r_dihedral_angle_1_deg8.008
r_angle_other_deg3.305
r_angle_refined_deg2.994
r_chiral_restr0.084
r_bond_other_d0.038
r_gen_planes_other0.023
r_bond_refined_d0.017
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms927
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms49

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing