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Cys-Gly dipeptidase GliJ in complex with Cu2+ and Zn2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LX0
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 3.35 63.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99 α = 90 b = 99 β = 90 c = 106.49 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 2017-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.37776 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 2.2 45 99.8 0.068 13.2 5.7 59136
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 2.3 99.9 0.505 2.8
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 5LX0 2.2 15 29360 1546 99.4 0.17733 0.17669 0.1827 0.18941 0.1945 RANDOM 53.959
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] 0.9 0.45 0.9 -2.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.983 r_sphericity_free 20.349 r_dihedral_angle_4_deg 14.123 r_dihedral_angle_3_deg 12.953 r_dihedral_angle_1_deg 5.33 r_sphericity_bonded 4.995 r_long_range_B_refined 1.73 r_long_range_B_other 1.622 r_mcangle_other 1.29 r_scangle_other 1.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.983 r_sphericity_free 20.349 r_dihedral_angle_4_deg 14.123 r_dihedral_angle_3_deg 12.953 r_dihedral_angle_1_deg 5.33 r_sphericity_bonded 4.995 r_long_range_B_refined 1.73 r_long_range_B_other 1.622 r_mcangle_other 1.29 r_scangle_other 1.275 r_scbond_it 1.216 r_scbond_other 1.216 r_mcangle_it 1.193 r_angle_refined_deg 1.073 r_mcbond_it 1.022 r_angle_other_deg 0.9 r_mcbond_other 0.82 r_rigid_bond_restr 0.413 r_chiral_restr 0.057 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 175 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing