6UIY

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 protein, 2.0 M ammonium sulfate, 0.1 M sodium acetate, pH 4
Crystal Properties
Matthews coefficientSolvent content
2.3246.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.74α = 90
b = 57.74β = 90
c = 184.27γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2018-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.00ALS8.2.1

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
11.4755.11000.0690.0720.020.99921.612.927259
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)
11.471.491000.5010.5290.170.9289.6

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 REPLACEMENTTHROUGHOUT2QCB1.4755.125837138399.940.1540.15280.1768RANDOM17.436
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]
0.040.04-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.298
r_dihedral_angle_4_deg15.426
r_dihedral_angle_3_deg14.08
r_dihedral_angle_1_deg6.976
r_angle_other_deg3.725
r_angle_refined_deg2.434
r_chiral_restr0.134
r_bond_other_d0.038
r_bond_refined_d0.018
r_gen_planes_other0.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.298
r_dihedral_angle_4_deg15.426
r_dihedral_angle_3_deg14.08
r_dihedral_angle_1_deg6.976
r_angle_other_deg3.725
r_angle_refined_deg2.434
r_chiral_restr0.134
r_bond_other_d0.038
r_bond_refined_d0.018
r_gen_planes_other0.017
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms935
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms75

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing