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Structure of E.coli GlpG in complex with peptide derived inhibitor Ac-RVRHA-phenylethyl-ketoamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XOV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 2M sodium chloride
Crystal Properties Matthews coefficient Solvent content 3.5 64.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.71 α = 90 b = 111.71 β = 90 c = 124.229 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-F 2015-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9794 Diamond I02
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 2.16 52.31 99.4 0.08 10.2 4.7 16097
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.16 2.23 99.6 0.72 0.559 1.9 4.6
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 2XOV 2.16 52.31 15315 781 99.32 0.21598 0.21355 0.2182 0.26593 0.2663 RANDOM 47.458
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] -0.35 -0.18 -0.35 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.811 r_long_range_B_refined 12.753 r_long_range_B_other 12.748 r_dihedral_angle_3_deg 12.716 r_scangle_other 11.056 r_dihedral_angle_4_deg 9.941 r_scbond_it 9.273 r_scbond_other 9.267 r_mcangle_it 7.296 r_mcangle_other 7.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.811 r_long_range_B_refined 12.753 r_long_range_B_other 12.748 r_dihedral_angle_3_deg 12.716 r_scangle_other 11.056 r_dihedral_angle_4_deg 9.941 r_scbond_it 9.273 r_scbond_other 9.267 r_mcangle_it 7.296 r_mcangle_other 7.296 r_mcbond_it 6.951 r_mcbond_other 6.943 r_dihedral_angle_1_deg 6.019 r_angle_refined_deg 1.508 r_angle_other_deg 0.948 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1478 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement PHASER phasing XDS data reduction XDS data scaling Aimless data scaling