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Crystal structure of the ligand-binding region of the group III metabotropic glutamate receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EWK PDB ENTRY 1EWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 298 0.02M Citrate, 0.08M MES, 0.01M Glutamate, 2.2M ammonium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.52 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.431 α = 90 b = 92.431 β = 90 c = 114.332 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2004-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.3 100 100 0.112 0.106 5.4 8887 8887
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 3.3 3.48 100 0.54 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 1EWK 3.3 12 3 3 8036 8036 607 100 0.279 0.27369 0.26996 0.2648 0.32395 0.3234 RANDOM 41.703
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] 1.88 0.94 1.88 -2.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.973 r_scangle_it 4.091 r_scbond_it 2.584 r_mcangle_it 2.343 r_mcbond_it 1.24 r_angle_refined_deg 0.963 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.973 r_scangle_it 4.091 r_scbond_it 2.584 r_mcangle_it 2.343 r_mcbond_it 1.24 r_angle_refined_deg 0.963 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3293 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction CCP4 data scaling AMoRE phasing