5VDI

Crystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q Bound to AM-3607, Glycine, and Ivermectin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TINPDB ENTRY 5TIN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277200 mM calcium chloride, 22.5-27.5% PEG350 MME, 100 mM MES, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
4.4972.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.006α = 90
b = 136β = 90
c = 191.635γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002015-01-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-11.2827CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
13.15099.70.2036865697
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.2197.70.8967.5

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 5TIN3.15064390122498.40.2330.2320.256RANDOM61.87
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]
-11.3310.21.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.24
r_dihedral_angle_3_deg13.933
r_dihedral_angle_4_deg12.532
r_dihedral_angle_1_deg5.275
r_angle_refined_deg1.124
r_angle_other_deg0.751
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.24
r_dihedral_angle_3_deg13.933
r_dihedral_angle_4_deg12.532
r_dihedral_angle_1_deg5.275
r_angle_refined_deg1.124
r_angle_other_deg0.751
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13509
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms480

Software

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