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Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 200 mM Calcium Chloride, 22.5-27.5% PEG-350MME, 100 mM MES
Crystal Properties Matthews coefficient Solvent content 3.87 68.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.12 α = 90 b = 119.12 β = 90 c = 429.968 γ = 90
Symmetry Space Group P 43 21 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 CCD RAYONIX MX300-HS 2014-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.25 50 99.8 0.131 0.999 16.2 13.8 47335
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.37 98.6 1.061 0.74 2.3 10.4
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 4RIF 3.25 50 47335 2490 99.7 0.234 0.233 0.2288 0.254 0.2476 RANDOM 117.5
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] 4.49 4.49 -8.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.223 r_dihedral_angle_3_deg 15.233 r_dihedral_angle_4_deg 13.692 r_dihedral_angle_1_deg 5.574 r_mcangle_it 3.477 r_mcbond_it 2.1 r_mcbond_other 2.1 r_angle_refined_deg 1.048 r_angle_other_deg 0.747 r_chiral_restr 0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.223 r_dihedral_angle_3_deg 15.233 r_dihedral_angle_4_deg 13.692 r_dihedral_angle_1_deg 5.574 r_mcangle_it 3.477 r_mcbond_it 2.1 r_mcbond_other 2.1 r_angle_refined_deg 1.048 r_angle_other_deg 0.747 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13543 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing