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Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris, phosphate and Zn bound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 294 40mM KH2PO4, 20% Glycerol, 14% PEG8000, 2mM ZnCl2
Crystal Properties Matthews coefficient Solvent content 2.82 56.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.032 α = 90 b = 104.08 β = 90 c = 112.412 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 MARMOSAIC 225 mm CCD x-ray mirror 2015-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE BL-21 0.97947 RRCAT INDUS-2 BL-21
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 1.95 47.22 100 0.107 13.6 6.1 70802
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.99 99.9 0.798 2.4 6.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.95 45 67238 3488 99.88 0.17362 0.17171 0.1827 0.21087 0.2165 RANDOM 25.259
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] -0.15 0.06 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.696 r_dihedral_angle_4_deg 19.241 r_dihedral_angle_3_deg 13.307 r_dihedral_angle_1_deg 6.861 r_long_range_B_refined 4.649 r_long_range_B_other 4.62 r_scangle_other 3.359 r_angle_refined_deg 2.234 r_scbond_it 2.18 r_scbond_other 2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.696 r_dihedral_angle_4_deg 19.241 r_dihedral_angle_3_deg 13.307 r_dihedral_angle_1_deg 6.861 r_long_range_B_refined 4.649 r_long_range_B_other 4.62 r_scangle_other 3.359 r_angle_refined_deg 2.234 r_scbond_it 2.18 r_scbond_other 2.18 r_mcangle_other 2.155 r_mcangle_it 2.154 r_mcbond_it 1.514 r_mcbond_other 1.514 r_angle_other_deg 1.14 r_chiral_restr 0.147 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5966 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement Coot model building PHENIX model building PHASER phasing Aimless data scaling XDS data processing MAR345dtb data collection