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Crystal structure of GlpG in complex with peptide chloromethylketone inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IC8 PDB entry 2IC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M Tris, pH 8.5, 3 M sodium nitrate, 15% glycerol
Crystal Properties Matthews coefficient Solvent content 3.3 62.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.049 α = 90 b = 110.049 β = 90 c = 127.311 γ = 120
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 PILATUS 6M 2018-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.972 CHESS F1
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 2.3 76.33 99.1 0.097 13.3 10.6 13264
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 2.3 2.38 0.568
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 PDB entry 2IC8 2.3 50.01 12584 648 98.84 0.21983 0.21808 0.2231 0.25225 0.2511 RANDOM 59.113
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] -2.03 -1.01 -2.03 6.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.447 r_dihedral_angle_4_deg 27.817 r_dihedral_angle_3_deg 18.232 r_long_range_B_refined 13.504 r_dihedral_angle_1_deg 11.51 r_mcangle_it 8.817 r_scbond_it 7.834 r_mcbond_it 6.168 r_angle_refined_deg 2.39 r_chiral_restr 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.447 r_dihedral_angle_4_deg 27.817 r_dihedral_angle_3_deg 18.232 r_long_range_B_refined 13.504 r_dihedral_angle_1_deg 11.51 r_mcangle_it 8.817 r_scbond_it 7.834 r_mcbond_it 6.168 r_angle_refined_deg 2.39 r_chiral_restr 0.154 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1462 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing