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Crystal Structure of a GDP-4-keto-6-deoxy-D-mannose reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 35% pentaerythritol propoxylate (5/4 PO/OH), 100 mM Tris, 200 mM NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.76 55.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.882 α = 72.54 b = 55.744 β = 82.95 c = 79.244 γ = 75.61
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 MAR CCD 165 mm 2005-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 1.0 APS 5ID-B
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 1.82 29.8 96.6 0.076 13.4 64129 -3 28.9
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 1.82 1.89 95.2 0.43 3.7 6792
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 1rpn 1.82 29.79 60922 3207 100 0.16649 0.1648 0.1645 0.1989 0.1972 RANDOM 22.423
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] -0.11 -0.04 0.72 0.2 -0.3 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.509 r_dihedral_angle_4_deg 19.139 r_dihedral_angle_3_deg 13.678 r_dihedral_angle_1_deg 5.808 r_scangle_it 3.547 r_scbond_it 2.31 r_angle_refined_deg 1.476 r_mcangle_it 1.35 r_mcbond_it 0.877 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.509 r_dihedral_angle_4_deg 19.139 r_dihedral_angle_3_deg 13.678 r_dihedral_angle_1_deg 5.808 r_scangle_it 3.547 r_scbond_it 2.31 r_angle_refined_deg 1.476 r_mcangle_it 1.35 r_mcbond_it 0.877 r_nbtor_refined 0.302 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.208 r_symmetry_hbond_refined 0.207 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4810 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MrBUMP phasing