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The crystal structure of landomycin C-6 ketoreductase LanV 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 6.5 294 0.1M Bis-Tris Propane, 0.2M sodium acetate, 18% PEG3350K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.04 39.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.99 α = 90 b = 91.99 β = 90 c = 106.22 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 2.5 50 99.1 0.161 11.52 9.1 16419 16276 -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 2.5 2.56 93 0.998 1.87
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 2.5 69.54 15465 800 99 0.1776 0.17447 0.1756 0.23466 0.2347 RANDOM 37.292
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] -1.62 -1.62 3.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.507 r_dihedral_angle_3_deg 13.369 r_dihedral_angle_4_deg 11.097 r_dihedral_angle_1_deg 5.043 r_mcangle_it 2.388 r_scbond_it 2.004 r_mcbond_it 1.449 r_angle_refined_deg 1.334 r_chiral_restr 0.102 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.507 r_dihedral_angle_3_deg 13.369 r_dihedral_angle_4_deg 11.097 r_dihedral_angle_1_deg 5.043 r_mcangle_it 2.388 r_scbond_it 2.004 r_mcbond_it 1.449 r_angle_refined_deg 1.334 r_chiral_restr 0.102 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 3590 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 160
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction EDNA data collection XDS data reduction