2OKK | pdb_00002okk

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OKJ	PDB ENTRY 2OKJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293	20% ethanol, 100 mM MES, 10 mM 2-mercaptoethanol, 20 mM CaCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.251	α = 90
b = 99.057	β = 90
c = 120.009	γ = 90

Symmetry
Space Group	C 2 2 21

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)	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	37.19					20717

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	98.85				2995

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2OKJ	2.3	37.19	20648	1077	97.93	0.2	0.196	0.2124	0.256	0.2662	RANDOM	51.402

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]
-1.32			0.94		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.868
r_dihedral_angle_3_deg	17.64
r_dihedral_angle_4_deg	17.402
r_dihedral_angle_1_deg	5.799
r_scangle_it	5.202
r_scbond_it	3.756
r_mcangle_it	1.908
r_angle_refined_deg	1.352
r_mcbond_it	1.021
r_nbtor_refined	0.303
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.129
r_symmetry_hbond_refined	0.117
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3770
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	20

Software

Software
Software Name	Purpose
SCALA	data scaling
ADSC	data collection
HKL-2000	data reduction
CCP4	data scaling
PHASER	phasing
REFMAC	refinement