☰ Navigation Tabs
Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84A mutant) in complex with 1,25-dihydroxyvitamin D3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZBY PDB ENTRY 2ZBY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 283 26% PEG MME 2000, 0.1M BIS-TRIS, 0.2M sodium chloride, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.2 44.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.152 α = 90 b = 53.671 β = 90 c = 138.881 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 2007-04-11 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 1.9 20 100 0.056 26.6 7.2 32117 -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) 1.9 1.97 99.9 0.316 6.8 6.9
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 (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 2ZBY 1.9 19.74 30443 30443 1614 99.77 0.20017 0.19802 0.1985 0.24196 0.2429 RANDOM 20.704
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] 1.2 -0.57 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.832 r_dihedral_angle_4_deg 16.785 r_dihedral_angle_3_deg 11.982 r_dihedral_angle_1_deg 4.837 r_scangle_it 1.575 r_angle_refined_deg 1.099 r_scbond_it 0.978 r_mcangle_it 0.767 r_mcbond_it 0.44 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.832 r_dihedral_angle_4_deg 16.785 r_dihedral_angle_3_deg 11.982 r_dihedral_angle_1_deg 4.837 r_scangle_it 1.575 r_angle_refined_deg 1.099 r_scbond_it 0.978 r_mcangle_it 0.767 r_mcbond_it 0.44 r_nbtor_refined 0.295 r_symmetry_vdw_refined 0.205 r_nbd_refined 0.184 r_symmetry_hbond_refined 0.105 r_xyhbond_nbd_refined 0.099 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 3090 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing