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Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution with bound 25-hydroxyvitamin 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 7.5 293 0.1M calcium acetate, 10.8% PEG3350, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.75 55.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.173 α = 90 b = 171.8 β = 90 c = 189.143 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 210r 2008-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
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 50 100 0.077 32.5 7.4 170383 29.5
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 2.07 100 0.594 3.3 7 16867
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 45.6 161521 8447 99.98 0.19886 0.197 0.1992 0.23402 0.1977 RANDOM 30.419
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] 0.53 -0.23 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.19 r_dihedral_angle_4_deg 18.893 r_dihedral_angle_3_deg 14.984 r_dihedral_angle_1_deg 5.782 r_scangle_it 3.383 r_scbond_it 2.178 r_angle_refined_deg 1.548 r_mcangle_it 1.463 r_mcbond_it 0.92 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.19 r_dihedral_angle_4_deg 18.893 r_dihedral_angle_3_deg 14.984 r_dihedral_angle_1_deg 5.782 r_scangle_it 3.383 r_scbond_it 2.178 r_angle_refined_deg 1.548 r_mcangle_it 1.463 r_mcbond_it 0.92 r_nbtor_refined 0.303 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.168 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.102 r_metal_ion_refined 0.087 r_symmetry_metal_ion_refined 0.024 r_bond_refined_d 0.014 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_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 15555 Nucleic Acid Atoms Solvent Atoms 1319 Heterogen Atoms 406
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling