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Crystal structure of N-terminal domain (Creatinase/Prolidase like domain) of putative metallopeptidase from Corynebacterium diphtheriae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 0.2 M Ammonium acetate 0.1 M HEPES 7.5 45% 2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.86 56.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.013 α = 90 b = 82.588 β = 90 c = 104.102 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 2010-06-10 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 2.15 40 100 0.1 27 6.1 37532 37532 2 2 43.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.15 2.23 100
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.15 40 2 2 37356 35489 1867 98.67 0.21 0.2098 0.20742 0.204 0.25392 0.249 RANDOM 27.026
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] -0.89 1.75 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.786 r_dihedral_angle_4_deg 17.059 r_dihedral_angle_3_deg 16.254 r_dihedral_angle_1_deg 6.19 r_scangle_it 4.834 r_scbond_it 3.137 r_mcangle_it 1.893 r_angle_refined_deg 1.859 r_mcbond_it 1.053 r_angle_other_deg 1.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.786 r_dihedral_angle_4_deg 17.059 r_dihedral_angle_3_deg 16.254 r_dihedral_angle_1_deg 6.19 r_scangle_it 4.834 r_scbond_it 3.137 r_mcangle_it 1.893 r_angle_refined_deg 1.859 r_mcbond_it 1.053 r_angle_other_deg 1.028 r_mcbond_other 0.295 r_chiral_restr 0.111 r_bond_refined_d 0.023 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3768 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 22
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing SHELX model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing