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Crystal structure of rhomboid intramembrane protease GlpG in complex with peptide derived inhibitor Ac-FATA-cmk
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, SITTING DROP 9.5 293 10% PEG 8000, 0.1 M CHES pH 9.5, 0.2 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.93 68.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.31 α = 90 b = 98.31 β = 90 c = 65.25 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 2013-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0 ESRF ID29
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 2.9 51.79 99.9 8094 8086 -3 -3
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 2.9 3.003 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.9 51.79 8094 8086 405 99.9 0.1845 0.1845 0.18239 0.1874 0.22477 0.2217 RANDOM 54.105
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] -0.16 -0.08 -0.16 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.168 r_dihedral_angle_3_deg 15.125 r_dihedral_angle_4_deg 13.562 r_long_range_B_refined 8.246 r_long_range_B_other 8.246 r_scangle_other 7.246 r_dihedral_angle_1_deg 6.103 r_scbond_it 4.942 r_scbond_other 4.883 r_mcangle_it 4.604
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.168 r_dihedral_angle_3_deg 15.125 r_dihedral_angle_4_deg 13.562 r_long_range_B_refined 8.246 r_long_range_B_other 8.246 r_scangle_other 7.246 r_dihedral_angle_1_deg 6.103 r_scbond_it 4.942 r_scbond_other 4.883 r_mcangle_it 4.604 r_mcangle_other 4.602 r_mcbond_it 3.254 r_mcbond_other 3.251 r_angle_other_deg 2.742 r_angle_refined_deg 1.279 r_chiral_restr 0.07 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 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 1489 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 43
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction