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Crystal structure of uridylate kinase from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BND PDB ENTRY 2BND
Crystallization Crystal Properties Matthews coefficient Solvent content 2.78 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.136 α = 90 b = 127.627 β = 91.46 c = 93.181 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 2008-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 NSRRC BL13B1
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 2.45 30 99.6 0.06 21.3 3.7 62731 2 58.2
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 2.45 2.54 98.8 0.52 2.3 3.6
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 2BND 2.49 96.4 56433 2994 98.93 0.2163 0.21311 0.2097 0.27571 0.268 RANDOM 51.522
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] 0.92 -0.82 -0.48 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.786 r_dihedral_angle_4_deg 18.855 r_dihedral_angle_3_deg 18.409 r_dihedral_angle_1_deg 5.732 r_scangle_it 3.049 r_mcangle_it 2.236 r_scbond_it 1.747 r_mcbond_it 1.232 r_angle_refined_deg 1.208 r_rigid_bond_restr 0.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.786 r_dihedral_angle_4_deg 18.855 r_dihedral_angle_3_deg 18.409 r_dihedral_angle_1_deg 5.732 r_scangle_it 3.049 r_mcangle_it 2.236 r_scbond_it 1.747 r_mcbond_it 1.232 r_angle_refined_deg 1.208 r_rigid_bond_restr 0.945 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10464 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing