5TIO

Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RIF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277200 mM Calcium Chloride, 22.5-27.5% PEG-350MME, 100 mM MES
Crystal Properties
Matthews coefficientSolvent content
3.8768.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.12α = 90
b = 119.12β = 90
c = 429.968γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2014-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
13.255099.80.1310.99916.213.847335
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.253.3798.61.0610.742.310.4

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 REPLACEMENTTHROUGHOUT4RIF3.255047335249099.70.2340.2330.254RANDOM117.5
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]
4.494.49-8.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.223
r_dihedral_angle_3_deg15.233
r_dihedral_angle_4_deg13.692
r_dihedral_angle_1_deg5.574
r_mcangle_it3.477
r_mcbond_it2.1
r_mcbond_other2.1
r_angle_refined_deg1.048
r_angle_other_deg0.747
r_chiral_restr0.058
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.223
r_dihedral_angle_3_deg15.233
r_dihedral_angle_4_deg13.692
r_dihedral_angle_1_deg5.574
r_mcangle_it3.477
r_mcbond_it2.1
r_mcbond_other2.1
r_angle_refined_deg1.048
r_angle_other_deg0.747
r_chiral_restr0.058
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_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 Atoms13543
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms184

Software

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