2OKJ

The X-ray crystal structure of the 67kDa isoform of Glutamic Acid Decarboxylase (GAD67)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JS3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.329318% PEG8,000, 100 mM MES, pH 6.3, 10 mM 2-mercaptoethanol and 20 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2344.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.048α = 90
b = 62.739β = 106.68
c = 101.346γ = 90
Symmetry
Space GroupP 1 21 1

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)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
12.397.1393.70.04517.13.44228442284
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)
2.369.20.1944.42.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1js32.397.134228442271211893.380.1880.1860.222RANDOM25.208
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]
-0.4-2.110.08-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.656
r_dihedral_angle_4_deg15.647
r_dihedral_angle_3_deg15.429
r_dihedral_angle_1_deg5.554
r_scangle_it3.534
r_scbond_it2.294
r_mcangle_it1.528
r_angle_refined_deg1.148
r_mcbond_it0.864
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.656
r_dihedral_angle_4_deg15.647
r_dihedral_angle_3_deg15.429
r_dihedral_angle_1_deg5.554
r_scangle_it3.534
r_scbond_it2.294
r_mcangle_it1.528
r_angle_refined_deg1.148
r_mcbond_it0.864
r_nbtor_refined0.299
r_symmetry_vdw_refined0.22
r_nbd_refined0.189
r_xyhbond_nbd_refined0.124
r_symmetry_hbond_refined0.098
r_chiral_restr0.084
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7919
Nucleic Acid Atoms
Solvent Atoms359
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
PHASERphasing