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Crystal Structure of UreE from Helicobacter pylori (apo form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 295 17% PEG 8000, 0.1M Sodium Citrate pH 5.0, vapor diffusion, sitting drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.27 62.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.011 α = 90 b = 131.011 β = 90 c = 51.267 γ = 120
Symmetry Space Group P 64 2 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 MAR CCD 165 mm 2008-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 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 2.08 42.88 99.8 0.05 18.7 15.7 16040
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) 2.08 2.15 99.5 0.496 8.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.08 42.88 15182 802 99.48 0.22277 0.2211 0.2202 0.25488 0.2583 RANDOM 41.904
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] 1.65 0.82 1.65 -2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.74 r_dihedral_angle_3_deg 16.566 r_dihedral_angle_4_deg 15.089 r_dihedral_angle_1_deg 6.889 r_scangle_it 2.979 r_scbond_it 1.769 r_angle_refined_deg 1.309 r_mcangle_it 1.26 r_mcbond_it 0.746 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.74 r_dihedral_angle_3_deg 16.566 r_dihedral_angle_4_deg 15.089 r_dihedral_angle_1_deg 6.889 r_scangle_it 2.979 r_scbond_it 1.769 r_angle_refined_deg 1.309 r_mcangle_it 1.26 r_mcbond_it 0.746 r_nbtor_refined 0.301 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.216 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 1170 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction