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X-ray structure of Lactobacillus brevis alcohol dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NXQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 PEG 550 MME, Magnesium chloride, HEPES
Crystal Properties Matthews coefficient Solvent content 2.41 48.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.03 α = 90 b = 83.31 β = 90 c = 114.38 γ = 90
Symmetry Space Group P 21 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 4M 2018-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.968 ESRF MASSIF-3
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 1.482 47.15 98.17 0.06928 0.07317 0.02317 0.999 17.4 6.4 89189 882139 21.04
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 1.482 1.535 93.25 1.664 0.8101 0.5529 0.643 9.8 8439
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 1nxq 1.482 47.15 89164 4460 99.21 0.18126 0.18011 0.1848 0.20304 0.2079 RANDOM 20.919
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] -1.1 1.3 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.493 r_dihedral_angle_4_deg 23.356 r_dihedral_angle_3_deg 12.136 r_dihedral_angle_1_deg 6.681 r_long_range_B_refined 4.646 r_long_range_B_other 4.596 r_scangle_other 4.123 r_scbond_other 2.906 r_scbond_it 2.903 r_mcangle_it 2.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.493 r_dihedral_angle_4_deg 23.356 r_dihedral_angle_3_deg 12.136 r_dihedral_angle_1_deg 6.681 r_long_range_B_refined 4.646 r_long_range_B_other 4.596 r_scangle_other 4.123 r_scbond_other 2.906 r_scbond_it 2.903 r_mcangle_it 2.2 r_mcangle_other 2.2 r_angle_refined_deg 2.171 r_mcbond_other 1.715 r_mcbond_it 1.714 r_angle_other_deg 1.111 r_chiral_restr 0.14 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3742 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building