2HJG | pdb_00002hjg

The crystal structure of the B. subtilis YphC GTPase in complex with GDP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	290	0.2M sodium flouride, 20% (w/v) PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.711	α = 90
b = 65.045	β = 90
c = 110.61	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	MAR CCD 165 mm		2005-06-27	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	0.9794, 0.9797, 1.0094	SRS	PX10.1

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	2.5	30	99.9	0.098	17.8	6.8		16253	2	2

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)
	2.5	2.65	99		0.32	5.1	6.8

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	MAD	THROUGHOUT	2.5	19.96	15364	814	100	0.21815	0.21539	0.2504	0.27353	0.2866	RANDOM	41.463

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]
-2.29			-0.61		2.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.42
r_dihedral_angle_4_deg	19.1
r_dihedral_angle_3_deg	16.346
r_dihedral_angle_1_deg	12.283
r_scangle_it	2.644
r_scbond_it	1.863
r_mcbond_it	1.296
r_angle_refined_deg	1.251
r_mcangle_it	0.816
r_angle_other_deg	0.766
r_symmetry_vdw_other	0.249
r_nbd_refined	0.202
r_nbd_other	0.196
r_nbtor_refined	0.179
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.143
r_symmetry_vdw_refined	0.093
r_metal_ion_refined	0.089
r_nbtor_other	0.083
r_chiral_restr	0.071
r_mcbond_other	0.062
r_bond_refined_d	0.01
r_bond_other_d	0.006
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3147
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing