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Crystal structure of the ternary complex of GephE-ADP-Glycine receptor derived peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U91
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 0.1 Sodium acetate pH 4.5
18-36% MPD
Crystal Properties Matthews coefficient Solvent content 2.58 52.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.09 α = 90 b = 99.649 β = 90 c = 113.002 γ = 90
Symmetry Space Group I 2 2 2
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 2015-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9180 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.95 44.04 99.5 0.11 0.148 0.098 0.989 6.9 3.7 36353
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 99.4 0.527 0.704 0.463 0.698 2 3.5
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 4U91 1.95 30 34586 1758 99.35 0.1684 0.16612 0.1765 0.21142 0.219 RANDOM 30.966
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] -0.47 0.17 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.337 r_dihedral_angle_4_deg 19.734 r_dihedral_angle_3_deg 14.808 r_long_range_B_refined 8.677 r_long_range_B_other 8.677 r_dihedral_angle_1_deg 7.032 r_scangle_other 5.245 r_mcangle_it 4.39 r_mcangle_other 4.389 r_scbond_it 3.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.337 r_dihedral_angle_4_deg 19.734 r_dihedral_angle_3_deg 14.808 r_long_range_B_refined 8.677 r_long_range_B_other 8.677 r_dihedral_angle_1_deg 7.032 r_scangle_other 5.245 r_mcangle_it 4.39 r_mcangle_other 4.389 r_scbond_it 3.392 r_scbond_other 3.386 r_mcbond_it 2.85 r_mcbond_other 2.849 r_angle_refined_deg 1.627 r_angle_other_deg 1.417 r_chiral_restr 0.139 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.002 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 3305 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing