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Crystal structure of the NR3A ligand binding core complex with glycine at 1.58 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PB7 Pdb entry 1PB7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 0.1 M NaBr, 0.1 mM NaAcetate, 4% PEG 4000, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.892 α = 90 b = 97.568 β = 93.55 c = 59.901 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 300 mm CCD 2006-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97931 APS 22-ID
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 1.58 30 95.9 0.054 11.7 3.8 74941 74941 1 1
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 1.58 1.64 75.3 0.209 5.6 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1PB7 1.58 29.89 71208 71208 3768 95.89 0.14905 0.14905 0.14754 0.1499 0.17714 0.1799 RANDOM 13.485
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] -0.05 0.04 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.517 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 11.247 r_dihedral_angle_1_deg 5.004 r_scangle_it 2.385 r_mcangle_it 1.928 r_scbond_it 1.594 r_angle_refined_deg 1.46 r_mcbond_it 1.287 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.517 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 11.247 r_dihedral_angle_1_deg 5.004 r_scangle_it 2.385 r_mcangle_it 1.928 r_scbond_it 1.594 r_angle_refined_deg 1.46 r_mcbond_it 1.287 r_nbtor_refined 0.32 r_nbd_refined 0.248 r_symmetry_vdw_refined 0.246 r_xyhbond_nbd_refined 0.2 r_symmetry_hbond_refined 0.175 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 4492 Nucleic Acid Atoms Solvent Atoms 631 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing