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Structural analysis of the tripeptide-bound form of Helicobacter pylori Csd4, a D,L-carboxypeptidase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 296 0.2M calcium chloride, 0.1M HEPES-NaOH, 25%(w/v) polyethylene glycol 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.54 51.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.127 α = 90 b = 66.383 β = 90 c = 143.785 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 270 2013-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
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 1.55 50 95.7 71540 4.1 4.1
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 1.55 1.58 96.1
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 (All) 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 1.55 20 67862 3596 95.69 0.20149 0.20149 0.20015 0.1992 0.22673 0.2263 RANDOM 19.605
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] 0.51 -0.03 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.508 r_dihedral_angle_3_deg 13.387 r_dihedral_angle_4_deg 12.315 r_dihedral_angle_1_deg 6.611 r_angle_refined_deg 1.318 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.508 r_dihedral_angle_3_deg 13.387 r_dihedral_angle_4_deg 12.315 r_dihedral_angle_1_deg 6.611 r_angle_refined_deg 1.318 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3366 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 48
Software Software Software Name Purpose ADSC data collection AutoSol phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling