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The crystal structure of the antimycin pathway standalone ketoreductase, AntM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298.15 0.1 M citrate phosphate buffer, pH 4.2, 0.2 M NaCl, and 10% w/v PEG 3K
Crystal Properties Matthews coefficient Solvent content 2.16 43.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.897 α = 90 b = 87.897 β = 90 c = 116.262 γ = 120
Symmetry Space Group P 62 2 2
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 EIGER2 X 16M 2018-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 63.69 99.9 0.997 7.8 9 16855
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 0.752
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4osp 2.1 63.69 16085 770 99.826 0.216 0.2135 0.2136 0.2727 0.2728 43.35
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] 2.008 1.004 2.008 -6.515
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.224 r_dihedral_angle_4_deg 17.358 r_dihedral_angle_3_deg 14.022 r_lrange_other 11.723 r_lrange_it 11.717 r_dihedral_angle_1_deg 7.279 r_scangle_it 6.142 r_scangle_other 6.134 r_mcangle_it 4.901 r_mcangle_other 4.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.224 r_dihedral_angle_4_deg 17.358 r_dihedral_angle_3_deg 14.022 r_lrange_other 11.723 r_lrange_it 11.717 r_dihedral_angle_1_deg 7.279 r_scangle_it 6.142 r_scangle_other 6.134 r_mcangle_it 4.901 r_mcangle_other 4.9 r_scbond_it 4.336 r_scbond_other 4.336 r_mcbond_it 3.667 r_mcbond_other 3.651 r_angle_other_deg 2.516 r_angle_refined_deg 1.65 r_symmetry_xyhbond_nbd_refined 0.551 r_nbd_other 0.228 r_symmetry_nbd_other 0.222 r_nbd_refined 0.215 r_symmetry_nbd_refined 0.206 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.163 r_symmetry_nbtor_other 0.069 r_symmetry_xyhbond_nbd_other 0.067 r_chiral_restr 0.065 r_bond_other_d 0.037 r_gen_planes_other 0.011 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1776 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data reduction Aimless data scaling PHASER phasing