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Crystal structure of Helicobacter pylori UreE bound to Zn2+
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 4.0M sodium formate, 0.1M sodium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.11 60.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.343 α = 90 b = 109.343 β = 90 c = 280.343 γ = 120
Symmetry Space Group P 65 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 RAYONIX MX-225 2010-05-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 1.2818, 1.2832, 1.2765 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.52 50 99.9 0.092 22.4 9.4 34454 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.52 2.56 98.2 0.43 3.4 6.9 1654
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 MAD THROUGHOUT 2.521 19.83 33219 1051 99.94 0.20389 0.20261 0.1997 0.24484 0.2413 RANDOM 39.727
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] 0.12 0.06 0.12 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.397 r_dihedral_angle_4_deg 18.397 r_dihedral_angle_3_deg 17.946 r_dihedral_angle_1_deg 7.131 r_scangle_it 5.821 r_scbond_it 3.301 r_angle_refined_deg 1.909 r_mcangle_it 1.759 r_mcbond_it 0.902 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.397 r_dihedral_angle_4_deg 18.397 r_dihedral_angle_3_deg 17.946 r_dihedral_angle_1_deg 7.131 r_scangle_it 5.821 r_scbond_it 3.301 r_angle_refined_deg 1.909 r_mcangle_it 1.759 r_mcbond_it 0.902 r_chiral_restr 0.114 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4697 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 5
Software Software Software Name Purpose MxCuBE data collection Auto-Rickshaw phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling