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Crystal structure of mithramycin 3-side chain keto-reductase MtmW in complex with NAD+ and PEG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 19% PEG400, 0.1 M Hepes, 7.0, 0.2 M CaCl2.
Crystal Properties Matthews coefficient Solvent content 2.87 57.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.679 α = 90 b = 124.679 β = 90 c = 107.359 γ = 90
Symmetry Space Group P 4 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 CCD RAYONIX MX300-HS 2017-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.65 50 99.9 0.16 0.066 15.4 7.1 24728
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.7 100 0.809 0.329 7.3
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 6OVX 2.67 35 23344 1296 99.84 0.18332 0.18075 0.186 0.22848 0.2262 RANDOM 41.359
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] -2.54 -2.54 5.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.897 r_dihedral_angle_4_deg 17.668 r_dihedral_angle_3_deg 15.359 r_long_range_B_refined 7.014 r_long_range_B_other 7.004 r_dihedral_angle_1_deg 6.535 r_scangle_other 5.098 r_mcangle_it 3.972 r_mcangle_other 3.972 r_scbond_it 3.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.897 r_dihedral_angle_4_deg 17.668 r_dihedral_angle_3_deg 15.359 r_long_range_B_refined 7.014 r_long_range_B_other 7.004 r_dihedral_angle_1_deg 6.535 r_scangle_other 5.098 r_mcangle_it 3.972 r_mcangle_other 3.972 r_scbond_it 3.083 r_scbond_other 3.082 r_mcbond_it 2.447 r_mcbond_other 2.44 r_angle_refined_deg 1.451 r_angle_other_deg 1.212 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 4750 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing