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The crystal structure of alcohol dehydrogenase 10 from Candida magnoliae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 100mM MES pH 6.5, 40% PEG 200. Soaked 20mM 4R-hydroxyisophorone
Crystal Properties Matthews coefficient Solvent content 2.35 47.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.178 α = 90 b = 80.425 β = 90 c = 80.52 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 CCD MARMOSAIC 225 mm CCD 2016-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.872899 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 40.3 100 0.058 1 20.5 8.1 65173 16.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.65 99 0.779 0.767 2.6 8.2
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 3V2G 1.6 40.3 61925 3247 99.93 0.14729 0.14559 0.16 0.17963 0.1881 RANDOM 22.799
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] -0.27 1.16 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.842 r_dihedral_angle_4_deg 17.303 r_dihedral_angle_3_deg 14.126 r_long_range_B_refined 10.056 r_long_range_B_other 10.054 r_dihedral_angle_1_deg 7.144 r_scangle_other 5.735 r_scbond_it 3.9 r_scbond_other 3.9 r_mcangle_other 3.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.842 r_dihedral_angle_4_deg 17.303 r_dihedral_angle_3_deg 14.126 r_long_range_B_refined 10.056 r_long_range_B_other 10.054 r_dihedral_angle_1_deg 7.144 r_scangle_other 5.735 r_scbond_it 3.9 r_scbond_other 3.9 r_mcangle_other 3.116 r_mcangle_it 3.113 r_angle_refined_deg 2.292 r_mcbond_it 2.209 r_mcbond_other 2.2 r_angle_other_deg 1.164 r_chiral_restr 0.153 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 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 3517 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing