3IHU

Crystal structure of DNA binding protein (YP_298823.1) from Ralstonia eutropha JMP134 at 1.92 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.17	277	24.0000% polyethylene glycol 6000, 1.0000M lithium chloride, 0.1M TRIS pH 8.17, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.646	α = 90
b = 79.135	β = 102.08
c = 103.244	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-04-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97862,0.97799	SSRL	BL11-1

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	1.92	29.361	99.6	0.052	0.052	12.1	2.7		32709			34.581

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.97	100		0.556	0.556	1.4	2.7	2416

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.92	29.361	32709	1662	99.45	0.201	0.199	0.237	RANDOM	24.792

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]
1.53		-0.65	-1.3		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.627
r_dihedral_angle_4_deg	17.537
r_dihedral_angle_3_deg	14.736
r_dihedral_angle_1_deg	4.953
r_scangle_it	4.134
r_scbond_it	2.582
r_mcangle_it	1.547
r_angle_refined_deg	1.489
r_angle_other_deg	0.967
r_mcbond_it	0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.627
r_dihedral_angle_4_deg	17.537
r_dihedral_angle_3_deg	14.736
r_dihedral_angle_1_deg	4.953
r_scangle_it	4.134
r_scbond_it	2.582
r_mcangle_it	1.547
r_angle_refined_deg	1.489
r_angle_other_deg	0.967
r_mcbond_it	0.87
r_mcbond_other	0.232
r_chiral_restr	0.089
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3117
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	8

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.