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Crystal structure of the GluN1 N-terminal domain (NTD)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 protein in (20mM Tris-HCl pH 7.5, 150mM NaCl) was mixed 1:1 with 4M Formate and 20mM TCEP, temperature 277K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 4.5 72.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.679 α = 90 b = 164.679 β = 90 c = 147.258 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 IMAGE PLATE RIGAKU RAXIS IV++ Rigaku VariMax HR 2010-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 3.4 142.6 99.9 0.15 12.9 6 32023 32023
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) 3.4 3.46 100 0.63 2.8 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD,SIRAS THROUGHOUT 3.4 45.24 32023 30371 1617 99.8 0.23185 0.22936 0.2249 0.27929 0.2741 RANDOM 75.057
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] -0.18 -0.09 -0.18 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.409 r_dihedral_angle_3_deg 20.175 r_dihedral_angle_4_deg 16.282 r_dihedral_angle_1_deg 6.144 r_angle_refined_deg 1.269 r_scangle_it 1.127 r_mcangle_it 0.63 r_scbond_it 0.615 r_mcbond_it 0.335 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.409 r_dihedral_angle_3_deg 20.175 r_dihedral_angle_4_deg 16.282 r_dihedral_angle_1_deg 6.144 r_angle_refined_deg 1.269 r_scangle_it 1.127 r_mcangle_it 0.63 r_scbond_it 0.615 r_mcbond_it 0.335 r_chiral_restr 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8725 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 218
Software Software Software Name Purpose HKL-2000 data collection SHARP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling