2ZEJ | pdb_00002zej

Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	30% PEG 4000, 100mM MgCl2, 0.1M Tris, 5mM GTP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.438	α = 81.51
b = 44.404	β = 69
c = 53.681	γ = 78.71

Symmetry
Space Group	P 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 315		2007-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97948	APS	19-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	50	93.1	0.126	16.9	4		23675			29.1

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)
1	2	2.03	62.3		0.398	1.8	1.9	793

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2	38.8	22346	1192	93.09	0.20156	0.19874	0.2016	0.25306	0.2547	RANDOM	34.29

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]
0.31	-0.16	-0.43	-0.59	-0.38	0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.987
r_dihedral_angle_4_deg	20.346
r_dihedral_angle_3_deg	20.045
r_dihedral_angle_1_deg	15.908
r_scangle_it	4.627
r_scbond_it	3.497
r_angle_refined_deg	2.145
r_mcangle_it	1.736
r_mcbond_it	1.206
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.987
r_dihedral_angle_4_deg	20.346
r_dihedral_angle_3_deg	20.045
r_dihedral_angle_1_deg	15.908
r_scangle_it	4.627
r_scbond_it	3.497
r_angle_refined_deg	2.145
r_mcangle_it	1.736
r_mcbond_it	1.206
r_nbtor_refined	0.305
r_chiral_restr	0.27
r_symmetry_hbond_refined	0.222
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.202
r_xyhbond_nbd_refined	0.139
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2538
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	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.