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Structure of Helicobacter pylori Csd3 from the orthorhombic crystal
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 296 160 mM ammonium sulfate, 80 mM sodium acetate, pH 4.6, 20% (v/v) PEG 4000, 20% (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.33 47.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.618 α = 90 b = 112.146 β = 90 c = 112.939 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 315 2013-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99.5 51535 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2 50 51535 51535 2756 99.52 0.20589 0.20322 0.2098 0.25591 0.2608 RANDOM 37.167
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] 1.08 -0.19 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.926 r_dihedral_angle_4_deg 17.833 r_dihedral_angle_3_deg 15.624 r_dihedral_angle_1_deg 7.268 r_long_range_B_refined 6.824 r_long_range_B_other 6.824 r_scangle_other 5.021 r_mcangle_it 3.884 r_mcangle_other 3.883 r_scbond_it 3.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.926 r_dihedral_angle_4_deg 17.833 r_dihedral_angle_3_deg 15.624 r_dihedral_angle_1_deg 7.268 r_long_range_B_refined 6.824 r_long_range_B_other 6.824 r_scangle_other 5.021 r_mcangle_it 3.884 r_mcangle_other 3.883 r_scbond_it 3.221 r_scbond_other 3.22 r_mcbond_it 2.703 r_mcbond_other 2.703 r_angle_refined_deg 1.577 r_angle_other_deg 0.777 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5822 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 77
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling