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Crystal structure of the NR3A ligand binding core complex with ACPC at 1.96 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RC7 Pdb entry 2RC7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 293 0.2 M Mg Acetate, 0.1 M NaCitrate, 14% PEG 3350, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.675 α = 90 b = 103.552 β = 95.04 c = 59.798 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 2007-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00000 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 1.96 40 97.9 0.088 8.5 2.9 43239 43239 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.03 96.4 0.362 0.0259 2.7
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 2RC7 1.96 19.91 40128 40128 2106 97.85 0.15921 0.15921 0.15646 0.158 0.21114 0.2111 RANDOM 14.799
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] -0.01 0.04 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.757 r_dihedral_angle_4_deg 17.032 r_dihedral_angle_3_deg 13.966 r_dihedral_angle_1_deg 6.089 r_scangle_it 3.513 r_scbond_it 2.241 r_angle_refined_deg 1.45 r_mcangle_it 1.383 r_mcbond_it 0.861 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.757 r_dihedral_angle_4_deg 17.032 r_dihedral_angle_3_deg 13.966 r_dihedral_angle_1_deg 6.089 r_scangle_it 3.513 r_scbond_it 2.241 r_angle_refined_deg 1.45 r_mcangle_it 1.383 r_mcbond_it 0.861 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.28 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 4524 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing