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Crystal structure of uroporphyrinogen-III synthetase from Helicobacter pylori 26695
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 12% peg3350, 0.1 M Na malonate ph 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.27 45.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.407 α = 90 b = 57.676 β = 90 c = 74.624 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315r mirrors 2010-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-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 2.1 35 100 0.11 22 5.9 14570 14570 2 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) 2.1 2.18 100 0.56 2.8 6 1412
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.1 35 2 2 14570 13733 729 99.22 0.21 0.20418 0.20217 0.24108 0.2305 RANDOM 30.458
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] -0.04 -0.02 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.909 r_dihedral_angle_4_deg 16.443 r_dihedral_angle_3_deg 14.376 r_dihedral_angle_1_deg 5.818 r_scangle_it 3.522 r_scbond_it 2.098 r_angle_refined_deg 1.266 r_mcangle_it 1.23 r_mcbond_it 0.64 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.909 r_dihedral_angle_4_deg 16.443 r_dihedral_angle_3_deg 14.376 r_dihedral_angle_1_deg 5.818 r_scangle_it 3.522 r_scbond_it 2.098 r_angle_refined_deg 1.266 r_mcangle_it 1.23 r_mcbond_it 0.64 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 1691 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 7
Software Software Software Name Purpose SBC-Collect data collection Auto-Rickshaw phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling