3HWU | pdb_00003hwu

Crystal structure of Putative DNA-binding protein (YP_299413.1) from Ralstonia eutrophA JMP134 at 1.30 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	277	0.2000M NaCl, 20.0000% PEG-1000, 0.1M Na,K-Phosphate pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.89	35.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.897	α = 90
b = 53.897	β = 90
c = 111.1	γ = 120

Symmetry
Space Group	H 3

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	Flat collimating mirror, toroid focusing mirror	2009-03-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97929,0.97918	SSRL	BL9-2

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	1.3	26.948	91.6	0.028	13.78	2.71		29085		-3	11.177

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	1.3	1.35	64		0.258	2.4

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	1.3	26.948	29085	1490	98.58	0.121	0.119	0.12	0.14	0.14	RANDOM	15.307

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]
0.2	0.1		0.2		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.949
r_dihedral_angle_3_deg	12.956
r_dihedral_angle_4_deg	11.397
r_sphericity_free	9.758
r_dihedral_angle_1_deg	6.584
r_scangle_it	4.475
r_sphericity_bonded	3.917
r_scbond_it	3.431
r_mcangle_it	2.304
r_rigid_bond_restr	1.899
r_mcbond_it	1.833
r_angle_refined_deg	1.644
r_angle_other_deg	0.845
r_mcbond_other	0.719
r_symmetry_vdw_other	0.312
r_symmetry_hbond_refined	0.308
r_nbd_other	0.207
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.197
r_nbtor_refined	0.175
r_symmetry_vdw_refined	0.135
r_chiral_restr	0.103
r_nbtor_other	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1101
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing