5DN8

1.76 Angstrom Crystal Structure of GTP-binding Protein Der from Coxiella burnetii 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	2HJC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	Protein: 11.0 mg/ml, 0.25M Sodium chloride, 0.01M Tris-HCl pH 8.3, 10mM GDP, Screen: JSCG+ (H11), 0.2M Magnesium chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.275	α = 90
b = 98.443	β = 90
c = 107.968	γ = 90

Symmetry
Space Group	P 21 21 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	MARMOSAIC 325 mm CCD		2014-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.76	30	99.7	0.051	0.051	33.8	7.2		47308		-3

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	1.76	1.79	100		0.537	3.9	7.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2HJC	1.76	29.05	44856	2386	99.21	0.17295	0.17128	0.2044	RANDOM	39.181

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]
0.61			-0.85		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.989
r_dihedral_angle_4_deg	12.319
r_dihedral_angle_3_deg	10.239
r_long_range_B_refined	7.467
r_long_range_B_other	7.342
r_scangle_other	4.476
r_mcangle_it	3.218
r_dihedral_angle_1_deg	3.217
r_mcangle_other	3.217
r_scbond_other	2.816
r_scbond_it	2.812
r_mcbond_it	2.114
r_mcbond_other	2.108
r_angle_refined_deg	1.473
r_angle_other_deg	0.746
r_chiral_restr	0.084
r_gen_planes_refined	0.02
r_gen_planes_other	0.016
r_bond_refined_d	0.009
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3187
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction