6JZS

Structure of the Manganese Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan in complex with Pyridine


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, 100 uM Pyridine
Crystal Properties
Matthews coefficientSolvent content
2.5651.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.715α = 90
b = 146.129β = 96.87
c = 62.481γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2019-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.00000SPring-8BL26B1

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
11.6847.3399.70.120.130.050.9968.16.6118187
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)
11.681.7197.31.4271.580.6690.5271.15.4

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 REPLACEMENTTHROUGHOUT3WSP1.6847.33112258586799.630.18140.180.2091RANDOM27.758
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_deg34.461
r_dihedral_angle_4_deg17.752
r_dihedral_angle_3_deg14.089
r_dihedral_angle_1_deg6.529
r_angle_refined_deg2.228
r_angle_other_deg1.359
r_chiral_restr0.082
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.461
r_dihedral_angle_4_deg17.752
r_dihedral_angle_3_deg14.089
r_dihedral_angle_1_deg6.529
r_angle_refined_deg2.228
r_angle_other_deg1.359
r_chiral_restr0.082
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7310
Nucleic Acid Atoms
Solvent Atoms526
Heterogen Atoms200

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction