☰ Navigation Tabs
Crystal structure of retinol dehydratase in complex with all-trans-4-oxoretinol and inactive cofactor PAP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FMJ pdb entry 1FMJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 289 7.5% PEG4000, 0.1M Na Hepes, 0.05M calcium chloride, 4% glycerol, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.64 53.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.506 α = 90 b = 67.192 β = 111.85 c = 85.066 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV mirrors 2000-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.1 100 89 0.093 13.3 2.7 45373 -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) 2.1 2.15 96 0.408 2.4 2.5 3230
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1FMJ 2.1 15 40422 40422 3121 88.4 0.19853 0.19853 0.19564 0.23134 RANDOM 22.609
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] -0.52 -0.59 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.49 r_scangle_it 2.905 r_scbond_it 1.837 r_angle_refined_deg 1.588 r_mcangle_it 1.238 r_angle_other_deg 0.886 r_mcbond_it 0.701 r_symmetry_vdw_other 0.262 r_symmetry_vdw_refined 0.242 r_nbd_other 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.49 r_scangle_it 2.905 r_scbond_it 1.837 r_angle_refined_deg 1.588 r_mcangle_it 1.238 r_angle_other_deg 0.886 r_mcbond_it 0.701 r_symmetry_vdw_other 0.262 r_symmetry_vdw_refined 0.242 r_nbd_other 0.233 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.094 r_nbtor_other 0.085 r_metal_ion_refined 0.051 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5685 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing