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Crystal structure of E. coli lipopolysaccharide specific CMP-KDO synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VH1 PDB ENTRY 1VH1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 100mM sodium acetate, pH4.6, 250mM sodium sulfate, 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.93 57.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.47 α = 90 b = 77.18 β = 90.03 c = 143.63 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 315 2009-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 1.0 Diamond I02
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 47 97.8 0.06 16 3.7 46074 46074
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 2.51 2.57 97 0.346 4.97 3.8
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 1VH1 2.51 47 43817 2360 98.07 0.20055 0.19871 0.2056 0.23397 0.2356 RANDOM 45.485
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] 4.64 -0.02 0.65 -5.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.787 r_dihedral_angle_3_deg 18.892 r_dihedral_angle_4_deg 16.59 r_dihedral_angle_1_deg 6.112 r_scangle_it 2.2 r_scbond_it 1.412 r_angle_refined_deg 1.317 r_angle_other_deg 0.933 r_mcangle_it 0.872 r_mcbond_it 0.528
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.787 r_dihedral_angle_3_deg 18.892 r_dihedral_angle_4_deg 16.59 r_dihedral_angle_1_deg 6.112 r_scangle_it 2.2 r_scbond_it 1.412 r_angle_refined_deg 1.317 r_angle_other_deg 0.933 r_mcangle_it 0.872 r_mcbond_it 0.528 r_symmetry_vdw_other 0.243 r_nbd_refined 0.218 r_nbd_other 0.197 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.157 r_symmetry_vdw_refined 0.123 r_mcbond_other 0.097 r_nbtor_other 0.086 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7515 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling