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Crystal Structure of Human Retinal Short-Chain Dehydrogenase/Reductase 3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Magnesium Acetate, MPD, cacodylate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.115 α = 90 b = 98.823 β = 115.87 c = 167.463 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 CCD ADSC QUANTUM 4 2004-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.9794 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 30 92 0.117 0.117 9.1 3.2 176307 176307 34.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 0.648 0.706 0.706 1.8 2.4 17963
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.4 30 172629 172629 3559 91.88 0.18166 0.18166 0.18067 0.2467 0.22903 0.2628 RANDOM 5.147
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] 1.69 0.75 -2.41 1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.459 r_dihedral_angle_4_deg 20.4 r_dihedral_angle_3_deg 16.884 r_scangle_it 5.927 r_dihedral_angle_1_deg 5.808 r_scbond_it 4.158 r_mcangle_it 2.116 r_angle_refined_deg 1.505 r_mcbond_it 1.413 r_angle_other_deg 0.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.459 r_dihedral_angle_4_deg 20.4 r_dihedral_angle_3_deg 16.884 r_scangle_it 5.927 r_dihedral_angle_1_deg 5.808 r_scbond_it 4.158 r_mcangle_it 2.116 r_angle_refined_deg 1.505 r_mcbond_it 1.413 r_angle_other_deg 0.919 r_mcbond_other 0.346 r_symmetry_vdw_other 0.274 r_symmetry_hbond_refined 0.227 r_nbd_refined 0.206 r_nbd_other 0.186 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.171 r_symmetry_vdw_refined 0.154 r_chiral_restr 0.088 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.073 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29359 Nucleic Acid Atoms Solvent Atoms 1251 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing