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Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution
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, 13% PEG3350, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.378 α = 90 b = 172.467 β = 90 c = 189.873 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 1.0000 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 2.2 50 100 0.101 26 7.3 129009 27.9
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 2.24 99.8 0.499 2.86 6 6327
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 2.2 49.27 122448 6465 99.86 0.20275 0.20054 0.2018 0.24407 0.2006 RANDOM 34.106
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] 0.6 -0.37 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.2 r_dihedral_angle_4_deg 18.166 r_dihedral_angle_3_deg 16.363 r_dihedral_angle_1_deg 5.965 r_scangle_it 3.283 r_scbond_it 2.122 r_angle_refined_deg 1.557 r_mcangle_it 1.396 r_mcbond_it 0.854 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.2 r_dihedral_angle_4_deg 18.166 r_dihedral_angle_3_deg 16.363 r_dihedral_angle_1_deg 5.965 r_scangle_it 3.283 r_scbond_it 2.122 r_angle_refined_deg 1.557 r_mcangle_it 1.396 r_mcbond_it 0.854 r_nbtor_refined 0.295 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.135 r_chiral_restr 0.105 r_metal_ion_refined 0.068 r_symmetry_metal_ion_refined 0.062 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15550 Nucleic Acid Atoms Solvent Atoms 814 Heterogen Atoms 257
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling