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Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris in citrate condition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FKC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5 294 0.1 M Citric acid, 20% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.4 48.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.179 α = 90 b = 103.673 β = 90 c = 136.063 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 2013-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97947 RRCAT INDUS-2 PX-BL21
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 2.2 48.44 98.9 0.051 43.6 12.3 42175
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 2.2 2.27 91.2 0.099 20.8 8.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 4FKC 2.2 44.25 40022 2086 98.78 0.14957 0.14788 0.1567 0.18134 0.1853 RANDOM 13.464
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] -0.61 0.77 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.852 r_dihedral_angle_4_deg 19.176 r_dihedral_angle_3_deg 11.96 r_dihedral_angle_1_deg 5.719 r_long_range_B_refined 5.183 r_long_range_B_other 4.941 r_scangle_other 3.186 r_scbond_it 2.001 r_scbond_other 2 r_mcangle_it 1.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.852 r_dihedral_angle_4_deg 19.176 r_dihedral_angle_3_deg 11.96 r_dihedral_angle_1_deg 5.719 r_long_range_B_refined 5.183 r_long_range_B_other 4.941 r_scangle_other 3.186 r_scbond_it 2.001 r_scbond_other 2 r_mcangle_it 1.892 r_mcangle_other 1.892 r_angle_refined_deg 1.627 r_mcbond_it 1.175 r_mcbond_other 1.175 r_angle_other_deg 1.118 r_chiral_restr 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 5984 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement Coot model building PHENIX model building PHASER phasing XDS data processing MAR345dtb data collection