☰ Navigation Tabs
Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84A mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZBX PDB ENTRY 2ZBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 277 20% PEG 8000, 0.1M bis-Tris-propane, 0.2M sodium chloride, 50mM lithium nitrate, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.25 45.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.437 α = 90 b = 53.586 β = 90 c = 141.339 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 2007-05-19 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 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 1.6 20 99.4 0.004 26.5 7.9 54213 -3 30.3
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) 1.6 1.66 96.5 0.329 5 6.5 5192
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2ZBX 1.6 19.83 51395 51395 2726 99.43 0.19741 0.19741 0.19615 0.1966 0.22154 0.2201 RANDOM 24.184
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] 0.94 -0.69 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.764 r_dihedral_angle_4_deg 16.679 r_dihedral_angle_3_deg 12.635 r_dihedral_angle_1_deg 5.123 r_scangle_it 2.637 r_scbond_it 1.679 r_angle_refined_deg 1.22 r_mcangle_it 1.113 r_mcbond_it 0.673 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.764 r_dihedral_angle_4_deg 16.679 r_dihedral_angle_3_deg 12.635 r_dihedral_angle_1_deg 5.123 r_scangle_it 2.637 r_scbond_it 1.679 r_angle_refined_deg 1.22 r_mcangle_it 1.113 r_mcbond_it 0.673 r_nbtor_refined 0.302 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.082 r_bond_refined_d 0.009 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 3068 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing