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Crystal structure of human Dipeptidyl Peptidase III
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CSK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 20% PEG3350. 0.2M MgForm, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.41 49.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.812 α = 90 b = 151.378 β = 100.04 c = 53.721 γ = 90
Symmetry Space Group P 1 21 1
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 2008-12-14 M SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.28267 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 100 100 0.107 0.107 7.1 4.8 61597 61597 21.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.78 0.78 1.93 3.7 3070
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 3CSK 1.9 75.59 60520 60520 925 99.49 0.17234 0.17234 0.17163 0.1715 0.21939 0.219 RANDOM 21.114
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 -1.05 0.63 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.662 r_dihedral_angle_4_deg 17.709 r_dihedral_angle_3_deg 12.628 r_dihedral_angle_1_deg 5.35 r_scangle_it 3.256 r_scbond_it 2.051 r_mcangle_it 1.239 r_angle_refined_deg 1.218 r_mcbond_it 0.761 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.662 r_dihedral_angle_4_deg 17.709 r_dihedral_angle_3_deg 12.628 r_dihedral_angle_1_deg 5.35 r_scangle_it 3.256 r_scbond_it 2.051 r_mcangle_it 1.239 r_angle_refined_deg 1.218 r_mcbond_it 0.761 r_nbtor_refined 0.304 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.119 r_chiral_restr 0.087 r_metal_ion_refined 0.016 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 5634 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms 4
Software Software Software Name Purpose HKL-3000 data collection PHASES phasing REFMAC refinement Coot model building HKL-3000 data reduction HKL-3000 data scaling