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Time-resolved structural snapshot of proteolysis by GlpG inside the membrane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F5D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M Na-acetate pH 5.5, 3 M NaCl, and 5 % ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.28 α = 90 b = 99.88 β = 90 c = 63.18 γ = 90
Symmetry Space Group C 2 2 21
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 2017-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.977 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 58.02 99.7 5.2 4.1 10314
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38
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 5F5D 2.4 58.02 8659 460 99.67 0.23682 0.23624 0.2363 0.24758 0.2479 RANDOM 49.135
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] 9.62 -6.67 -2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.411 r_dihedral_angle_3_deg 17.248 r_dihedral_angle_4_deg 12.808 r_long_range_B_refined 9.387 r_dihedral_angle_1_deg 6.119 r_mcangle_it 5.671 r_scbond_it 4.584 r_mcbond_it 3.772 r_angle_refined_deg 1.455 r_chiral_restr 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.411 r_dihedral_angle_3_deg 17.248 r_dihedral_angle_4_deg 12.808 r_long_range_B_refined 9.387 r_dihedral_angle_1_deg 6.119 r_mcangle_it 5.671 r_scbond_it 4.584 r_mcbond_it 3.772 r_angle_refined_deg 1.455 r_chiral_restr 0.13 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 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 1433 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing