6E7T

Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QEL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52903.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Crystal Properties
Matthews coefficientSolvent content
3.2762.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 268.594α = 90
b = 59.835β = 116.86
c = 146.015γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-20.9100NSLS-II17-ID-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.3150910.0920.1070.0547.73.683106
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.312.3548.10.6060.770.4670.6571.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3QEL2.312567430352077.630.19530.19370.225RANDOM42.339
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]
0.231-2.430.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.17
r_dihedral_angle_4_deg21.363
r_dihedral_angle_3_deg15.479
r_dihedral_angle_1_deg7.965
r_angle_other_deg0.41
r_angle_refined_deg0.363
r_chiral_restr0.035
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.17
r_dihedral_angle_4_deg21.363
r_dihedral_angle_3_deg15.479
r_dihedral_angle_1_deg7.965
r_angle_other_deg0.41
r_angle_refined_deg0.363
r_chiral_restr0.035
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.002
r_bond_refined_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10701
Nucleic Acid Atoms
Solvent Atoms317
Heterogen Atoms232

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing