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Crystal Structure of Ferric Cytochrome P450cam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CPP PDB ENTRY 2CPP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 298 11-14% PEG 4000, 50mM Tris-HCl, 250mM KCl, 1mM d-camphor, 10mM dithioerythritol(DTE), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.7 54.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.522 α = 90 b = 63.522 β = 90 c = 249.67 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD Bruker DIP-6040 2007-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.7 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 31.77 99.5 0.064 8.7 7.1 68576 68576 15.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.66 100 0.35 5.58 7.1 6730
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2CPP 1.6 31.77 65093 3403 99.57 0.16595 0.16506 0.164 0.18272 0.1819 RANDOM 16.766
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.286 r_dihedral_angle_4_deg 14.226 r_dihedral_angle_3_deg 13.228 r_dihedral_angle_1_deg 5.385 r_sphericity_bonded 2.836 r_scangle_it 2.71 r_scbond_it 1.744 r_angle_refined_deg 1.502 r_mcangle_it 1.131 r_mcbond_it 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.286 r_dihedral_angle_4_deg 14.226 r_dihedral_angle_3_deg 13.228 r_dihedral_angle_1_deg 5.385 r_sphericity_bonded 2.836 r_scangle_it 2.71 r_scbond_it 1.744 r_angle_refined_deg 1.502 r_mcangle_it 1.131 r_mcbond_it 0.66 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.214 r_metal_ion_refined 0.154 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3531 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing