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Crystal structure of mithramycin 3-side chain keto-reductase MtmW in complex with NAD+, P422 form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 1mM NADP+ (with protein), reservoir: 16% PEG 1500, 0.1M Na-Citrate, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.85 56.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.479 α = 90 b = 124.479 β = 90 c = 107.066 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 MARMOSAIC 300 mm CCD 2015-02-13 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) 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 50 99.9 0.111 23.7 9.6 49578
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 2.1 2.14 99.4 0.673 9
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 6OVQ 2.1 35 46759 2489 99.22 0.20622 0.20486 0.2129 0.2321 0.2418 RANDOM 38.802
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] -2.48 -2.48 4.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.461 r_dihedral_angle_4_deg 14.959 r_dihedral_angle_3_deg 12.388 r_dihedral_angle_1_deg 6.421 r_long_range_B_refined 5.21 r_long_range_B_other 5.183 r_scangle_other 3.756 r_mcangle_it 2.821 r_mcangle_other 2.82 r_scbond_it 2.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.461 r_dihedral_angle_4_deg 14.959 r_dihedral_angle_3_deg 12.388 r_dihedral_angle_1_deg 6.421 r_long_range_B_refined 5.21 r_long_range_B_other 5.183 r_scangle_other 3.756 r_mcangle_it 2.821 r_mcangle_other 2.82 r_scbond_it 2.355 r_scbond_other 2.355 r_mcbond_it 1.849 r_mcbond_other 1.849 r_angle_refined_deg 1.329 r_angle_other_deg 1.244 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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 4540 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing