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Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution with bound vitamin D3
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 0.1M calcium acetate, 12% PEG3350, pH7.5, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.76 55.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.384 α = 90 b = 172.266 β = 90 c = 189.063 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 270 2009-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
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 2.05 50 100 0.107 26.9 7.4 158815 23.3
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) 2.05 2.09 99.8 0.54 2.9 6.3 7805
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 2.05 49.09 150738 7866 99.91 0.20308 0.20114 0.2033 0.23955 0.2026 RANDOM 28.916
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] 0.54 -0.09 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.946 r_dihedral_angle_4_deg 17.251 r_dihedral_angle_3_deg 15.189 r_dihedral_angle_1_deg 5.67 r_scangle_it 3.161 r_scbond_it 2.048 r_angle_refined_deg 1.5 r_mcangle_it 1.327 r_mcbond_it 1.062 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.946 r_dihedral_angle_4_deg 17.251 r_dihedral_angle_3_deg 15.189 r_dihedral_angle_1_deg 5.67 r_scangle_it 3.161 r_scbond_it 2.048 r_angle_refined_deg 1.5 r_mcangle_it 1.327 r_mcbond_it 1.062 r_nbtor_refined 0.299 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.188 r_symmetry_vdw_refined 0.166 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.102 r_metal_ion_refined 0.097 r_symmetry_metal_ion_refined 0.034 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15550 Nucleic Acid Atoms Solvent Atoms 1030 Heterogen Atoms 397
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling