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Cys-Gly dipeptidase GliJ (space group P3221)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ITQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.1 M MES pH 6.0, 5 % isopropanol
Crystal Properties Matthews coefficient Solvent content 3.45 64.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.01 α = 90 b = 100.01 β = 90 c = 107.15 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS EIGER X 16M 2016-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.738 SLS X06SA
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 2.4 45 99.5 0.062 18.9 7.6 46680
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 2.4 2.5 96.1 0.239 3.6
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 1ITQ 2.4 15 23274 1225 99.24 0.17269 0.17147 0.1785 0.1949 0.2027 RANDOM 53.347
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] 0.51 0.26 0.51 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.22 r_sphericity_free 24.232 r_dihedral_angle_3_deg 13.762 r_sphericity_bonded 12.632 r_dihedral_angle_4_deg 12.139 r_dihedral_angle_1_deg 5.66 r_long_range_B_refined 2.284 r_long_range_B_other 2.011 r_mcangle_it 1.481 r_mcangle_other 1.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.22 r_sphericity_free 24.232 r_dihedral_angle_3_deg 13.762 r_sphericity_bonded 12.632 r_dihedral_angle_4_deg 12.139 r_dihedral_angle_1_deg 5.66 r_long_range_B_refined 2.284 r_long_range_B_other 2.011 r_mcangle_it 1.481 r_mcangle_other 1.481 r_scangle_other 1.307 r_mcbond_it 1.103 r_mcbond_other 1.102 r_scbond_other 1.092 r_scbond_it 1.091 r_angle_refined_deg 1.078 r_angle_other_deg 0.896 r_rigid_bond_restr 0.721 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3007 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing