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The crystal structure of angucycline C-6 ketoreductase LanV with bound NADP and 11-deoxy-6-oxylandomycinone
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 6.5 294 0.1M Bis-Tris-Propane, 0.2M sodium acetate, 18% PEG3350 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K
Crystal Properties Matthews coefficient Solvent content 2.07 40.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.61 α = 90 b = 92.61 β = 90 c = 106.33 γ = 90
Symmetry Space Group P 41 21 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 225 mm CCD mirrors 2011-10-27 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 50 99.1 0.137 12.07 7.2 31692 -3 31.971
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 2.05 90.9 0.929 2.12 6.9 2137
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 50 31680 1598 98.96 0.1845 0.1823 0.1832 0.2249 0.2269 RANDOM 27.0109
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] -0.86 -0.86 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.519 r_dihedral_angle_4_deg 14.491 r_dihedral_angle_3_deg 13.47 r_dihedral_angle_1_deg 5.048 r_angle_refined_deg 1.366 r_chiral_restr 0.106 r_bond_refined_d 0.009 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3697 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 151
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection EDNA data collection XDS data reduction