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The crystal structure of urdamycin C-6 ketoreductase domain UrdMred with bound NADP and rabelomycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KWH PDB entry 4KWH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 294 0.1M BisTris, 0.2M ammonium acetate, 17% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.3 46.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.44 α = 90 b = 110.33 β = 110.35 c = 78.07 γ = 90
Symmetry Space Group P 1 21 1
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 mirrors 2012-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2.25 50 99.6 0.124 13.16 4.7 48206 47995 -3
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 2.25 2.3 96.9 0.903 1.78
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 PDB entry 4KWH 2.25 50 45391 2418 99.93 0.19683 0.1942 0.1952 0.24623 0.2471 RANDOM 34.216
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] -1.99 -0.43 0.79 1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.41 r_dihedral_angle_4_deg 17.114 r_dihedral_angle_3_deg 15.106 r_dihedral_angle_1_deg 5.469 r_mcangle_it 2.725 r_scbond_it 2.011 r_mcbond_it 1.625 r_angle_refined_deg 0.97 r_chiral_restr 0.066 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.41 r_dihedral_angle_4_deg 17.114 r_dihedral_angle_3_deg 15.106 r_dihedral_angle_1_deg 5.469 r_mcangle_it 2.725 r_scbond_it 2.011 r_mcbond_it 1.625 r_angle_refined_deg 0.97 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7375 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 73
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction EDNA data collection XDS data reduction