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Alcohol dehydrogenase ADH-'A' from Rhodococcus ruber DSM 44541 at pH 8.5 in complex with NAD and butane-1,4-diol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JV7 PDB ENTRY 3JV7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 100 MM BISTRIS PROPANE BUFFER PH 8.5, 20% (W/V) PEG MW 4000, 5 MM CDCL2, 6% V/V 2-PROPANOL, 5% (V/V) 1, 4-BUTANEDIOL. PROTEIN AT 10 MG/ML
Crystal Properties Matthews coefficient Solvent content 2.68 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.674 α = 90 b = 105.1 β = 91.27 c = 109.176 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 287 CCD ADSC CCD 2009-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 2.8 109.5 9 0.1 7.5 3.6 34356 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 2.8 2.87 87.3 0.36 2 3.1
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 3JV7 2.8 109.15 34356 1807 98.69 0.1916 0.18816 0.1869 0.25756 0.2515 RANDOM 38.43
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] -2.79 0.94 3.02 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.413 r_dihedral_angle_4_deg 17.264 r_dihedral_angle_3_deg 17.195 r_dihedral_angle_1_deg 6.403 r_scangle_it 2.422 r_angle_refined_deg 1.635 r_scbond_it 1.42 r_mcangle_it 0.947 r_mcbond_it 0.503 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.413 r_dihedral_angle_4_deg 17.264 r_dihedral_angle_3_deg 17.195 r_dihedral_angle_1_deg 6.403 r_scangle_it 2.422 r_angle_refined_deg 1.635 r_scbond_it 1.42 r_mcangle_it 0.947 r_mcbond_it 0.503 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other 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 9731 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing