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Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84F mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZBZ PDB ENTRY 2ZBZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 283 16% PEGMME 2000, 10% MPD, 0.1M Bis-tris, 0.2M sodium chloride, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.16 43.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.5 α = 90 b = 53.384 β = 90 c = 138.97 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 2007-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.00 SPring-8 BL44B2
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 20 99.4 0.073 23.1 5.3 27037 -3 17.7
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) 2 2.07 98.2 0.191 8.3 5.4 2617
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2ZBZ 2 20 25633 1378 99.34 0.18356 0.18112 0.22992 0.2269 RANDOM 18.306
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] 0.66 -1.05 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.887 r_dihedral_angle_4_deg 15.994 r_dihedral_angle_3_deg 12.796 r_dihedral_angle_1_deg 5.473 r_scangle_it 2.972 r_scbond_it 1.849 r_angle_refined_deg 1.271 r_mcangle_it 1.189 r_mcbond_it 0.71 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.887 r_dihedral_angle_4_deg 15.994 r_dihedral_angle_3_deg 12.796 r_dihedral_angle_1_deg 5.473 r_scangle_it 2.972 r_scbond_it 1.849 r_angle_refined_deg 1.271 r_mcangle_it 1.189 r_mcbond_it 0.71 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.202 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.168 r_symmetry_hbond_refined 0.154 r_chiral_restr 0.089 r_bond_refined_d 0.011 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_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 3107 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing