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Crystal structure of Helicobacter pylori UreE bound to Ni2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TJ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 4.0M sodium formate, 0.1M sodium acetate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 51.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.552 α = 90 b = 117.145 β = 90 c = 98.665 γ = 90
Symmetry Space Group C 2 2 21
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 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91885 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 1.59 58.57 97.9 0.049 24.9 8.4 51702 51702 -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 1.59 1.62 87.7 0.448 2.6 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3TJ8 1.591 58.57 48955 48955 2629 97.69 0.18629 0.18498 0.1836 0.21115 0.2093 RANDOM 33.1
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] 0.36 0.19 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.032 r_dihedral_angle_4_deg 15.308 r_dihedral_angle_3_deg 15.191 r_scangle_it 6.235 r_dihedral_angle_1_deg 6.101 r_scbond_it 4.027 r_angle_refined_deg 2.576 r_mcangle_it 2.523 r_mcbond_it 1.641 r_chiral_restr 0.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.032 r_dihedral_angle_4_deg 15.308 r_dihedral_angle_3_deg 15.191 r_scangle_it 6.235 r_dihedral_angle_1_deg 6.101 r_scbond_it 4.027 r_angle_refined_deg 2.576 r_mcangle_it 2.523 r_mcbond_it 1.641 r_chiral_restr 0.187 r_bond_refined_d 0.031 r_gen_planes_refined 0.014 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 2342 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 31
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling