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Crystal Structure of UreE from Helicobacter pylori (metal of unknown identity bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L9Z UreE in apo form (PDB code 3L9Z)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 295 16% PEG 8000, 5% glycerol, 0.1M Sodium Citrate pH 5.0, vapor diffusion, sitting drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.39 48.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.557 α = 90 b = 85.557 β = 90 c = 202.574 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 MAR165 2008-12-19 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
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 2.86 45.06 99.4 0.12 8.7 23.3 18190
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) 2.86 2.96 97.3 0.347 9.7
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 UreE in apo form (PDB code 3L9Z) 2.86 45.06 17182 926 99.31 0.27957 0.27817 0.275 0.30486 0.299 RANDOM 63.314
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] 2.09 2.09 -4.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.458 r_dihedral_angle_4_deg 22.68 r_dihedral_angle_3_deg 20.595 r_dihedral_angle_1_deg 8.08 r_scangle_it 5.211 r_scbond_it 2.959 r_mcangle_it 2.43 r_angle_refined_deg 1.844 r_mcbond_it 1.351 r_symmetry_vdw_refined 0.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.458 r_dihedral_angle_4_deg 22.68 r_dihedral_angle_3_deg 20.595 r_dihedral_angle_1_deg 8.08 r_scangle_it 5.211 r_scbond_it 2.959 r_mcangle_it 2.43 r_angle_refined_deg 1.844 r_mcbond_it 1.351 r_symmetry_vdw_refined 0.421 r_nbtor_refined 0.324 r_nbd_refined 0.263 r_symmetry_hbond_refined 0.22 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 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 4413 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing