☰ Navigation Tabs
Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (wild type) with imidazole bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Starting model was obtained by MAD phasing using iron atom as a anomalous scatterer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 283 24% PEG 8000, 0.1M imidazole, 0.2M sodium chloride, 0.2M sodium formate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.21 44.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.575 α = 90 b = 53.754 β = 90 c = 140.948 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 90 CCD ADSC QUANTUM 210 mirrors 2006-09-23 M SINGLE WAVELENGTH 2 1 x-ray 90 CCD ADSC QUANTUM 210 mirrors 2005-10-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0000 SPring-8 BL44B2 2 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.7377, 1.7403, 1.7310, 1.7240 SPring-8 BL44B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.5 20 97.1 0.035 32.3 9 62925 -3 25.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.53 91.1 0.264 7.4 8.1 2863
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD and MOLECULAR REPLACEMENT THROUGHOUT Starting model was obtained by MAD phasing using iron atom as a anomalous scatterer 1.5 19.62 59532 59532 3180 96.82 0.19578 0.19578 0.19434 0.1914 0.22327 0.2192 RANDOM 18.555
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] 0.7 -0.61 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.441 r_dihedral_angle_4_deg 15.114 r_dihedral_angle_3_deg 12.269 r_dihedral_angle_1_deg 4.865 r_scangle_it 2.788 r_scbond_it 1.852 r_angle_refined_deg 1.254 r_mcangle_it 1.167 r_mcbond_it 0.739 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.441 r_dihedral_angle_4_deg 15.114 r_dihedral_angle_3_deg 12.269 r_dihedral_angle_1_deg 4.865 r_scangle_it 2.788 r_scbond_it 1.852 r_angle_refined_deg 1.254 r_mcangle_it 1.167 r_mcbond_it 0.739 r_nbtor_refined 0.304 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.123 r_xyhbond_nbd_refined 0.12 r_symmetry_hbond_refined 0.12 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3072 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling SHARP phasing