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Crystal structure of the ketone reductase ChKRED20 from the genome of Chryseobacterium sp. CA49
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NI5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M NaCl, 0.1M HEPES, 1.6M (NH4)2SO4, PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.33 47.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.826 α = 90 b = 102.867 β = 90 c = 109.38 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 6M 2016-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9754 SSRF BL18U1
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 1.85 29.7 99.3 0.1 19.1 6.7 83764
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 1.85 1.88 98.6 0.635 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 4NI5 1.85 29.7 79619 4080 99.15 0.1963 0.19451 0.2034 0.22993 0.2378 RANDOM 40.306
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] -2.98 3.24 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.756 r_dihedral_angle_4_deg 14.919 r_dihedral_angle_3_deg 14.332 r_dihedral_angle_1_deg 6.376 r_long_range_B_refined 5.956 r_long_range_B_other 5.945 r_scangle_other 5.004 r_mcangle_it 3.563 r_mcangle_other 3.563 r_scbond_it 3.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.756 r_dihedral_angle_4_deg 14.919 r_dihedral_angle_3_deg 14.332 r_dihedral_angle_1_deg 6.376 r_long_range_B_refined 5.956 r_long_range_B_other 5.945 r_scangle_other 5.004 r_mcangle_it 3.563 r_mcangle_other 3.563 r_scbond_it 3.46 r_scbond_other 3.46 r_mcbond_it 2.789 r_mcbond_other 2.789 r_angle_refined_deg 1.573 r_angle_other_deg 0.991 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 7332 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing