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Cys-Gly dipeptidase GliJ in complex with Ca2+
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 3.32 62.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.65 α = 90 b = 98.65 β = 90 c = 106.45 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 2017-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 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 99.2 0.073 14.4 6.8 30637
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 99.8 0.535 3.8
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 28995 1526 98.87 0.18019 0.1793 0.1845 0.1969 0.2021 RANDOM 54.028
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] 1.22 0.61 1.22 -3.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.149 r_sphericity_free 22.073 r_dihedral_angle_4_deg 13.61 r_dihedral_angle_3_deg 13.179 r_sphericity_bonded 6.427 r_dihedral_angle_1_deg 5.665 r_long_range_B_refined 2.208 r_long_range_B_other 1.926 r_mcangle_other 1.595 r_scangle_other 1.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.149 r_sphericity_free 22.073 r_dihedral_angle_4_deg 13.61 r_dihedral_angle_3_deg 13.179 r_sphericity_bonded 6.427 r_dihedral_angle_1_deg 5.665 r_long_range_B_refined 2.208 r_long_range_B_other 1.926 r_mcangle_other 1.595 r_scangle_other 1.498 r_mcangle_it 1.475 r_mcbond_it 1.317 r_scbond_it 1.316 r_scbond_other 1.315 r_mcbond_other 1.083 r_angle_refined_deg 1.075 r_angle_other_deg 0.893 r_rigid_bond_restr 0.665 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 3014 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing