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Structural analysis of the mDAP-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 2.55 51.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.931 α = 90 b = 66.668 β = 90 c = 143.997 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 CCD ADSC QUANTUM 210r 2013-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.2823 PAL/PLS 7A (6B, 6C1)
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 1.41 50 95.7 94978 2.1 2.1
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 1.41 1.43 91.9
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 1.41 50 87286 4610 92.65 0.19056 0.19056 0.18942 0.1898 0.21188 0.2123 RANDOM 21.705
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] 1.02 -0.19 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.316 r_dihedral_angle_3_deg 14.116 r_dihedral_angle_4_deg 13.492 r_long_range_B_refined 8.63 r_long_range_B_other 8.629 r_dihedral_angle_1_deg 6.609 r_scangle_other 2.184 r_mcangle_other 1.681 r_mcangle_it 1.68 r_scbond_it 1.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.316 r_dihedral_angle_3_deg 14.116 r_dihedral_angle_4_deg 13.492 r_long_range_B_refined 8.63 r_long_range_B_other 8.629 r_dihedral_angle_1_deg 6.609 r_scangle_other 2.184 r_mcangle_other 1.681 r_mcangle_it 1.68 r_scbond_it 1.315 r_angle_refined_deg 1.306 r_scbond_other 1.305 r_mcbond_it 1.004 r_mcbond_other 0.999 r_angle_other_deg 0.777 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 3365 Nucleic Acid Atoms Solvent Atoms 708 Heterogen Atoms 40
Software Software Software Name Purpose ADSC data collection AutoSol phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling