6JVC

Structure of the Cobalt Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WSP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE293PEG8000, Magnesium Chloride, Tris-HCl, 0.5% DMSO, 125 uM N-Abietoyl-L-Tryptophan
Crystal Properties
Matthews coefficientSolvent content
2.6253.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.898α = 90
b = 148.247β = 98.02
c = 63.219γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.00000SPring-8BL41XU

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
11.7549.4299.80.1160.1260.0490.9958.96.7107592
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)
11.751.781001.5291.6510.6160.5061.27.1

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 REPLACEMENTTHROUGHOUT3WSP1.7547.87102228531999.790.18740.18570.2203RANDOM27.509
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.262
r_dihedral_angle_4_deg16.234
r_dihedral_angle_3_deg14.045
r_dihedral_angle_1_deg6.949
r_angle_refined_deg2.033
r_angle_other_deg1.418
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.262
r_dihedral_angle_4_deg16.234
r_dihedral_angle_3_deg14.045
r_dihedral_angle_1_deg6.949
r_angle_refined_deg2.033
r_angle_other_deg1.418
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7335
Nucleic Acid Atoms
Solvent Atoms579
Heterogen Atoms416

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction