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Crystal Structure of Camphor Soaked 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); After crystallization, soaked camphor saturated buffer for 2 days, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.71 54.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.608 α = 90 b = 63.608 β = 90 c = 250.389 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 Si 2008-04-22 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 1.3 34.9 98.6 0.075 34.4 4.9 125182 15.597
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) 1.3 1.35 98.9 0.407 4.9 5 12324
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 1.3 34.9 118839 6277 98.63 0.16644 0.16552 0.1638 0.18386 0.1819 RANDOM 16.699
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.319 r_dihedral_angle_4_deg 14.211 r_dihedral_angle_3_deg 12.511 r_sphericity_bonded 5.878 r_dihedral_angle_1_deg 5.585 r_scangle_it 2.34 r_scbond_it 1.566 r_angle_refined_deg 1.5 r_angle_other_deg 1.354 r_mcangle_it 1.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.319 r_dihedral_angle_4_deg 14.211 r_dihedral_angle_3_deg 12.511 r_sphericity_bonded 5.878 r_dihedral_angle_1_deg 5.585 r_scangle_it 2.34 r_scbond_it 1.566 r_angle_refined_deg 1.5 r_angle_other_deg 1.354 r_mcangle_it 1.039 r_rigid_bond_restr 0.607 r_mcbond_it 0.575 r_symmetry_vdw_other 0.275 r_nbtor_refined 0.24 r_nbd_other 0.22 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.204 r_nbtor_other 0.175 r_mcbond_other 0.155 r_metal_ion_refined 0.137 r_symmetry_hbond_refined 0.12 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 Atoms Number Protein Atoms 4715 Nucleic Acid Atoms Solvent Atoms 806 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing