2QBM

Crystal structure of the P450cam G248T mutant in the cyanide bound state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AKDPDB entry 1akd

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42771 UL OF 15 MG/ML P450 IN 50 MM Potassium phosphate, 250 MM KCL WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION (100 mM Tris, 250 mM KCl, 27-30% PEG 8000, 100 MM DTE), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2846.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.8α = 90
b = 64.6β = 90
c = 105.5γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHDYNAMICALLY BENDABLE MIRROR2007-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9796SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.820990.05519.15.54067640676-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.9950.4253.54.8

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1akd1.819.94406753864120341000.17850.176270.22045RANDOM24.505
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]
0.950.54-1.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.383
r_dihedral_angle_3_deg14.497
r_dihedral_angle_4_deg12.967
r_dihedral_angle_1_deg5.781
r_scangle_it3.946
r_scbond_it2.503
r_angle_refined_deg1.554
r_mcangle_it1.453
r_mcbond_it0.771
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.383
r_dihedral_angle_3_deg14.497
r_dihedral_angle_4_deg12.967
r_dihedral_angle_1_deg5.781
r_scangle_it3.946
r_scbond_it2.503
r_angle_refined_deg1.554
r_mcangle_it1.453
r_mcbond_it0.771
r_nbtor_refined0.306
r_nbd_refined0.241
r_xyhbond_nbd_refined0.154
r_symmetry_vdw_refined0.147
r_symmetry_hbond_refined0.132
r_metal_ion_refined0.118
r_chiral_restr0.115
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms3215
Nucleic Acid Atoms
Solvent Atoms416
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
XSCALEdata scaling
CNSphasing