3TMZ

Crystal Structure of P450 2B4(H226Y) in complex with Amlodipine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MVRPDB ENTRY 3MVR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72911M K/Na tartarate, 0.1 M Tris, 0.2M Li2SO4, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.5265.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.995α = 90
b = 92.995β = 90
c = 152.773γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2010-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.98SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.24838.93898.10.0430.0436.23704936346
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.2482.3789.80.4980.4981.53.34755

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3MVR2.24838.933520033933178696.40.193640.193640.19060.25059RANDOM48.995
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]
-0.04-0.02-0.040.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.053
r_dihedral_angle_3_deg16.615
r_dihedral_angle_4_deg16.371
r_dihedral_angle_1_deg6.944
r_scangle_it4.842
r_scbond_it3.066
r_mcangle_it2.129
r_angle_refined_deg2.085
r_mcbond_it1.17
r_chiral_restr0.194
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.053
r_dihedral_angle_3_deg16.615
r_dihedral_angle_4_deg16.371
r_dihedral_angle_1_deg6.944
r_scangle_it4.842
r_scbond_it3.066
r_mcangle_it2.129
r_angle_refined_deg2.085
r_mcbond_it1.17
r_chiral_restr0.194
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3694
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms133

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
autoXDSdata reduction
SCALAdata scaling