☰ Navigation Tabs
Crystal structure of the kainate receptor GluK4 ligand binding domain in complex with kainate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 15 % glycerol, 25.5 % PEG4000, 0.17 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.2 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.5 α = 90 b = 69.87 β = 90 c = 162.76 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 PILATUS3 2M 2015-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
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 2.05 40.69 99.3 0.136 8.9 5.8 16260 23.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 96.3 0.709 2 5.5
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 2XXT 2.05 40.69 15326 897 99.11 0.19494 0.19099 0.2617 0.2377 RANDOM 26.711
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] 0.21 0.08 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.144 r_dihedral_angle_4_deg 18.375 r_dihedral_angle_3_deg 15.398 r_long_range_B_refined 6.899 r_long_range_B_other 6.729 r_dihedral_angle_1_deg 6.332 r_scangle_other 4.576 r_mcangle_it 3.251 r_mcangle_other 3.249 r_scbond_it 2.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.144 r_dihedral_angle_4_deg 18.375 r_dihedral_angle_3_deg 15.398 r_long_range_B_refined 6.899 r_long_range_B_other 6.729 r_dihedral_angle_1_deg 6.332 r_scangle_other 4.576 r_mcangle_it 3.251 r_mcangle_other 3.249 r_scbond_it 2.919 r_scbond_other 2.914 r_mcbond_it 2.131 r_mcbond_other 2.131 r_angle_refined_deg 1.805 r_angle_other_deg 1.078 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 1995 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PHENIX refinement xia2 data reduction XDS data reduction PHASER phasing Coot model building