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Structure of cytochrome P450 vdh from Pseudonocardia autotrophica (orthorhombic crystal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A4G PDB ENTRY 3A4G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 26% PEG1000, 0.1M Bis-tris, pH7.5, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.595 α = 90 b = 65.793 β = 90 c = 102.264 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 4r 2006-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
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 3.05 50 97.6 0.09 18.9 3.6 8366 8366 45
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) 3.05 3.16 97.9 0.317 6 3.8 822
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 3A4G 3.06 45.74 7852 430 97.01 0.21952 0.21672 0.2204 0.26978 0.2085 RANDOM 44.138
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] -3.82 7.4 -3.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.869 r_dihedral_angle_3_deg 16.494 r_dihedral_angle_4_deg 14.375 r_dihedral_angle_1_deg 4.343 r_angle_refined_deg 0.96 r_scangle_it 0.813 r_mcangle_it 0.585 r_scbond_it 0.46 r_mcbond_it 0.323 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.869 r_dihedral_angle_3_deg 16.494 r_dihedral_angle_4_deg 14.375 r_dihedral_angle_1_deg 4.343 r_angle_refined_deg 0.96 r_scangle_it 0.813 r_mcangle_it 0.585 r_scbond_it 0.46 r_mcbond_it 0.323 r_nbtor_refined 0.295 r_symmetry_vdw_refined 0.181 r_nbd_refined 0.18 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3094 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 44
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling