7LZ2

Structure of glutamate receptor-like channel GLR3.4 ligand-binding domain in complex with methionine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7LZ0PDB entry 7LZ0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2772 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.4649.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.581α = 90
b = 74.581β = 90
c = 508.887γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2020-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97918APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.5127.2299.90.0620.0640.0180.99919.313.2136052
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)
11.51.531001.181.2260.330.65413.6

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 REPLACEMENTTHROUGHOUTPDB entry 7LZ01.584.96129095670699.870.18590.18460.2091RANDOM26.087
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]
0.090.050.09-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.757
r_dihedral_angle_3_deg13.938
r_dihedral_angle_4_deg13.739
r_dihedral_angle_1_deg6.975
r_angle_refined_deg1.878
r_angle_other_deg1.479
r_chiral_restr0.095
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.757
r_dihedral_angle_3_deg13.938
r_dihedral_angle_4_deg13.739
r_dihedral_angle_1_deg6.975
r_angle_refined_deg1.878
r_angle_other_deg1.479
r_chiral_restr0.095
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5899
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms90

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction