2OKK

The X-ray crystal structure of the 65kDa isoform of Glutamic Acid Decarboxylase (GAD65)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OKJPDB ENTRY 2OKJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.229320% ethanol, 100 mM MES, 10 mM 2-mercaptoethanol, 20 mM CaCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0539.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.251α = 90
b = 99.057β = 90
c = 120.009γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.000APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.337.1920717
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4298.852995

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 2OKJ2.337.1920648107797.930.20.1960.256RANDOM51.402
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]
-1.320.940.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.868
r_dihedral_angle_3_deg17.64
r_dihedral_angle_4_deg17.402
r_dihedral_angle_1_deg5.799
r_scangle_it5.202
r_scbond_it3.756
r_mcangle_it1.908
r_angle_refined_deg1.352
r_mcbond_it1.021
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.868
r_dihedral_angle_3_deg17.64
r_dihedral_angle_4_deg17.402
r_dihedral_angle_1_deg5.799
r_scangle_it5.202
r_scbond_it3.756
r_mcangle_it1.908
r_angle_refined_deg1.352
r_mcbond_it1.021
r_nbtor_refined0.303
r_nbd_refined0.203
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.143
r_chiral_restr0.129
r_symmetry_hbond_refined0.117
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3770
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms20

Software

Software
Software NamePurpose
SCALAdata scaling
ADSCdata collection
HKL-2000data reduction
CCP4data scaling
PHASERphasing
REFMACrefinement