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apo structure of short-chain alcohol dehydrogenase from Ralstonia sp. DSM 6428
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FGS PDB ENTRY 4FGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.1M BIS-TRIS PROPANE PH 7.0 CONTAINING 20% (W/V) PEG 3350 AND 0.02 M SODIUM-POTASSIUM PHOSPHATE. THE PROTEIN CONCENTRATION WAS 24 MG ML-1.
Crystal Properties Matthews coefficient Solvent content 1.9 35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.48 α = 90 b = 52.51 β = 116.57 c = 151.47 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC CCD 2013-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.52 60.86 97.7 0.03 15.6 3.3 149646 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.57 96.8 0.25 4.9 3.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4FGS 1.5 60.86 141654 7501 96.94 0.15962 0.15812 0.1695 0.18784 0.196 RANDOM 21.997
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 0.12 1.87 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.71 r_dihedral_angle_4_deg 11.306 r_dihedral_angle_3_deg 11.088 r_dihedral_angle_1_deg 6.344 r_scbond_it 3.091 r_mcangle_it 2.88 r_mcbond_it 2.124 r_mcbond_other 2.123 r_angle_refined_deg 2.122 r_angle_other_deg 1.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.71 r_dihedral_angle_4_deg 11.306 r_dihedral_angle_3_deg 11.088 r_dihedral_angle_1_deg 6.344 r_scbond_it 3.091 r_mcangle_it 2.88 r_mcbond_it 2.124 r_mcbond_other 2.123 r_angle_refined_deg 2.122 r_angle_other_deg 1.683 r_chiral_restr 0.131 r_bond_refined_d 0.022 r_gen_planes_refined 0.013 r_bond_other_d 0.011 r_gen_planes_other 0.008 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6877 Nucleic Acid Atoms Solvent Atoms 847 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing