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Crystal structure of the ternary complex of GephE-ADP-GABA(A) receptor derived peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium acetate pH 4.5
18-36 % MPD
Crystal Properties Matthews coefficient Solvent content 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.962 α = 90 b = 99.217 β = 90 c = 111.608 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 2M 2015-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 1.55 43.48 98.7 0.074 0.095 0.06 0.997 9.6 4.5 69059
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 1.55 1.58 97.8 0.734 0.974 0.592 0.655 1.6 4.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4U90 1.55 30 65584 3466 98.49 0.16083 0.15903 0.19575 0.1961 RANDOM 29.037
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] 0.77 -0.16 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.695 r_dihedral_angle_4_deg 19.261 r_dihedral_angle_3_deg 15.392 r_long_range_B_refined 7.696 r_long_range_B_other 7.695 r_dihedral_angle_1_deg 7.029 r_scangle_other 5.246 r_mcangle_other 3.684 r_mcangle_it 3.683 r_scbond_it 3.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.695 r_dihedral_angle_4_deg 19.261 r_dihedral_angle_3_deg 15.392 r_long_range_B_refined 7.696 r_long_range_B_other 7.695 r_dihedral_angle_1_deg 7.029 r_scangle_other 5.246 r_mcangle_other 3.684 r_mcangle_it 3.683 r_scbond_it 3.563 r_scbond_other 3.515 r_mcbond_it 2.614 r_mcbond_other 2.566 r_angle_refined_deg 1.833 r_angle_other_deg 1.488 r_chiral_restr 0.128 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 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 3291 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing