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Cys-Gly dipeptidase GliJ (space group C2)
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 3.42 64.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.8 α = 90 b = 100.25 β = 90.27 c = 106.64 γ = 90
Symmetry Space Group C 1 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 2016-08-20 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 2.1 45 97.7 0.044 13.8 3.1 103656
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 2.1 2.2 97.8 0.481 2.1
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 2.1 15 98193 5168 97.42 0.1686 0.16711 0.176 0.19721 0.2057 RANDOM 51.672
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] 0.12 0.04 1.34 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.946 r_sphericity_free 23.401 r_sphericity_bonded 14.323 r_dihedral_angle_3_deg 13.859 r_dihedral_angle_4_deg 13.661 r_dihedral_angle_1_deg 6.024 r_long_range_B_refined 2.547 r_long_range_B_other 2.547 r_mcangle_it 1.961 r_mcangle_other 1.961
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.946 r_sphericity_free 23.401 r_sphericity_bonded 14.323 r_dihedral_angle_3_deg 13.859 r_dihedral_angle_4_deg 13.661 r_dihedral_angle_1_deg 6.024 r_long_range_B_refined 2.547 r_long_range_B_other 2.547 r_mcangle_it 1.961 r_mcangle_other 1.961 r_scangle_other 1.839 r_mcbond_it 1.488 r_mcbond_other 1.486 r_scbond_it 1.479 r_scbond_other 1.478 r_angle_refined_deg 1.144 r_angle_other_deg 0.912 r_rigid_bond_restr 0.571 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 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 9035 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing