2IL1 | pdb_00002il1

Crystal structure of a predicted human GTPase in complex with GDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G17	PDB entry 1G17, chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	291	22% PEG4000, 0.2M calcium acetate, 0.1M sodium cacodylate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.5	51.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.463	α = 90
b = 45.463	β = 90
c = 315.454	γ = 120

Symmetry
Space Group	P 65 2 2

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	MARMOSAIC 300 mm CCD		2006-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97625	APS	22-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	94.2	0.052	13.1	13.9		13543

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	2.07		52.3	0.43		2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB entry 1G17, chain A	2.1	30	12316	615	99.467	0.2412	0.27	0.2661	0.3	39.449

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]
-0.056	-0.028		-0.056		0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.483
r_dihedral_angle_4_deg	15.609
r_dihedral_angle_3_deg	13.407
r_dihedral_angle_1_deg	5.825
r_scangle_it	3.6
r_mcangle_it	3.245
r_scbond_it	2.74
r_mcbond_it	2.439
r_angle_refined_deg	1.415
r_nbtor_refined	0.294
r_symmetry_vdw_refined	0.241
r_metal_ion_refined	0.221
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.154
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.094
r_symmetry_metal_ion_refined	0.092
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1278
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	36

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data scaling
REFMAC	refinement
ARP/wARP	model building
MolProbity	model building
Coot	model building