2ZWU

Crystal Structure of Camphor Soaked Ferric Cytochrome P450cam


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CPPPDB ENTRY 2CPP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.429811-14% PEG 4000, 50mM Tris-HCl, 250mM KCl, 1mM d-camphor, 10mM dithioerythritol(DTE); After crystallization, soaked camphor saturated buffer for 2 days, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7154.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.608α = 90
b = 63.608β = 90
c = 250.389γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-6040Si2008-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.7SPring-8BL44XU

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
11.334.998.60.07534.44.912518215.597
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.31.3598.90.4074.9512324

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2CPP1.334.9118839627798.630.166440.165520.18386RANDOM16.699
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_deg33.319
r_dihedral_angle_4_deg14.211
r_dihedral_angle_3_deg12.511
r_sphericity_bonded5.878
r_dihedral_angle_1_deg5.585
r_scangle_it2.34
r_scbond_it1.566
r_angle_refined_deg1.5
r_angle_other_deg1.354
r_mcangle_it1.039
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.319
r_dihedral_angle_4_deg14.211
r_dihedral_angle_3_deg12.511
r_sphericity_bonded5.878
r_dihedral_angle_1_deg5.585
r_scangle_it2.34
r_scbond_it1.566
r_angle_refined_deg1.5
r_angle_other_deg1.354
r_mcangle_it1.039
r_rigid_bond_restr0.607
r_mcbond_it0.575
r_symmetry_vdw_other0.275
r_nbtor_refined0.24
r_nbd_other0.22
r_nbd_refined0.214
r_symmetry_vdw_refined0.204
r_nbtor_other0.175
r_mcbond_other0.155
r_metal_ion_refined0.137
r_symmetry_hbond_refined0.12
r_xyhbond_nbd_refined0.115
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_free
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4715
Nucleic Acid Atoms
Solvent Atoms806
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing