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Rhodococcus ruber Alcohol Dehydrogenase NADH Biomimetic Complex - Compound 4b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JV7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293.15 0.1M Sodium Citrate tribasic, pH 5.0, 30% Jeffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 3.77 67.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.295 α = 90 b = 158.177 β = 91.05 c = 272.938 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 298 CCD ADSC QUANTUM 210r 2022-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95372 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.99 49.18 99.5 0.152 0.179 0.094 0.985 6.2 3.5 133770
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.99 3.04 95.6 0.587 0.691 0.363 0.737 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.99 49.18 131738 2010 99.4 0.19384 0.19306 0.1933 0.24562 0.2441 RANDOM 39.986
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] 2.12 -0.77 -1.22 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.949 r_long_range_B_refined 9.15 r_dihedral_angle_1_deg 6.515 r_dihedral_angle_2_deg 6.302 r_mcangle_it 5.54 r_scbond_it 4.215 r_mcbond_it 3.407 r_angle_refined_deg 1.687 r_chiral_restr 0.108 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.949 r_long_range_B_refined 9.15 r_dihedral_angle_1_deg 6.515 r_dihedral_angle_2_deg 6.302 r_mcangle_it 5.54 r_scbond_it 4.215 r_mcbond_it 3.407 r_angle_refined_deg 1.687 r_chiral_restr 0.108 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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_it r_scangle_other 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 30087 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 291
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing