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)
Type	Source	Accession Code	Details
experimental model	PDB	1JS3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	293	18% 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 coefficient	Solvent content
2.23	44.83

Crystal Data

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

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2006-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.3	97.13	93.7	0.045	17.1	3.4	42284	42284

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3			69.2	0.194	4.4	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1js3	2.3	97.13	42284	42271	2118	93.38	0.188	0.186	0.222	RANDOM	25.208

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		-2.11	0.08		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.656
r_dihedral_angle_4_deg	15.647
r_dihedral_angle_3_deg	15.429
r_dihedral_angle_1_deg	5.554
r_scangle_it	3.534
r_scbond_it	2.294
r_mcangle_it	1.528
r_angle_refined_deg	1.148
r_mcbond_it	0.864
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.656
r_dihedral_angle_4_deg	15.647
r_dihedral_angle_3_deg	15.429
r_dihedral_angle_1_deg	5.554
r_scangle_it	3.534
r_scbond_it	2.294
r_mcangle_it	1.528
r_angle_refined_deg	1.148
r_mcbond_it	0.864
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.22
r_nbd_refined	0.189
r_xyhbond_nbd_refined	0.124
r_symmetry_hbond_refined	0.098
r_chiral_restr	0.084
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7919
Nucleic Acid Atoms
Solvent Atoms	359
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.