6MCW

Crystal structure of the P450 domain of the CYP51-ferredoxin fusion protein from Methylococcus capsulatus, complex with the detergent Anapoe-X-114


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6FMO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.4291PEG 6000, photassium phosphate, glycerol, TCEP
Crystal Properties
Matthews coefficientSolvent content
3.4864.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.685α = 90
b = 150.685β = 90
c = 66.321γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDFOCUSING MIRRORS2018-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.07807APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.430990.0540.1090.04317.66.233877
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.441000.8730.5751.46.4

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 REPLACEMENTTHROUGHOUT6FMO2.429.9632189167399.240.216890.215820.23722RANDOM58.303
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]
-0.83-0.41-0.832.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.993
r_dihedral_angle_4_deg18.308
r_dihedral_angle_3_deg17.601
r_long_range_B_other12.946
r_long_range_B_refined12.944
r_scangle_other8.961
r_dihedral_angle_1_deg8.256
r_mcangle_it7.79
r_mcangle_other7.788
r_scbond_other6.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.993
r_dihedral_angle_4_deg18.308
r_dihedral_angle_3_deg17.601
r_long_range_B_other12.946
r_long_range_B_refined12.944
r_scangle_other8.961
r_dihedral_angle_1_deg8.256
r_mcangle_it7.79
r_mcangle_other7.788
r_scbond_other6.071
r_scbond_it6.07
r_mcbond_it5.311
r_mcbond_other5.299
r_angle_refined_deg0.821
r_angle_other_deg0.817
r_chiral_restr0.253
r_gen_planes_refined0.014
r_gen_planes_other0.006
r_bond_refined_d0.001
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3609
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing