5E78

Crystal structure of P450 BM3 heme domain variant complexed with Co(III)Sep


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277100-160 mM MgCl2, 100 mM MES (pH 6.5) 10-18% PEG 3350 and 5-10 mM Co(III)Sep
Crystal Properties
Matthews coefficientSolvent content
2.7355.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.97α = 90
b = 128.54β = 90
c = 150.06γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8123EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
122098.650.0615.663.976758
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1196.43.710844

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 REPLACEMENTTHROUGHOUT2J4S22072920383898.510.176950.175090.21185RANDOM30.102
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]
0.85-0.8-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.919
r_dihedral_angle_4_deg18.261
r_dihedral_angle_3_deg13.53
r_long_range_B_refined8.549
r_long_range_B_other8.332
r_dihedral_angle_1_deg6.292
r_scangle_other5.741
r_scbond_it4.086
r_scbond_other4.054
r_mcangle_other3.614
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.919
r_dihedral_angle_4_deg18.261
r_dihedral_angle_3_deg13.53
r_long_range_B_refined8.549
r_long_range_B_other8.332
r_dihedral_angle_1_deg6.292
r_scangle_other5.741
r_scbond_it4.086
r_scbond_other4.054
r_mcangle_other3.614
r_mcangle_it3.611
r_mcbond_it2.752
r_mcbond_other2.746
r_angle_refined_deg1.576
r_angle_other_deg1.269
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.006
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 Atoms7253
Nucleic Acid Atoms
Solvent Atoms869
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASESphasing