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Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris, phosphate and Mn bound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 294 40mM KH2PO4, 20% Glycerol, 14% PEG 8000, 2mM MnCl2
Crystal Properties Matthews coefficient Solvent content 2.82 56.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.962 α = 90 b = 104.284 β = 90 c = 112.324 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 1.85 47.29 99.8 0.102 14 6.8 82603
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 1.85 1.89 99.4 0.871 2.4 6.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.85 45 78448 4080 99.73 0.16088 0.15907 0.19591 0.1892 RANDOM 24.237
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] -0.03 -0.34 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.829 r_dihedral_angle_4_deg 20.813 r_dihedral_angle_3_deg 12.548 r_dihedral_angle_1_deg 6.697 r_long_range_B_refined 4.971 r_long_range_B_other 4.889 r_scangle_other 3.459 r_angle_refined_deg 2.369 r_scbond_it 2.285 r_scbond_other 2.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.829 r_dihedral_angle_4_deg 20.813 r_dihedral_angle_3_deg 12.548 r_dihedral_angle_1_deg 6.697 r_long_range_B_refined 4.971 r_long_range_B_other 4.889 r_scangle_other 3.459 r_angle_refined_deg 2.369 r_scbond_it 2.285 r_scbond_other 2.284 r_mcangle_other 1.9 r_mcangle_it 1.899 r_mcbond_it 1.383 r_mcbond_other 1.383 r_angle_other_deg 1.161 r_chiral_restr 0.155 r_bond_refined_d 0.027 r_gen_planes_refined 0.015 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 5988 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement Coot model building PHENIX model building PHASER phasing Aimless data scaling XDS data processing MAR345dtb data collection