4M34

Crystal structure of gated-pore mutant D138H of second DNA-Binding protein under starvation from Mycobacterium smegmatis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z90

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch under oil	6.5	298	100mM MgCl2, 0.1M sodium cacodylate, 20% PEG3350, pH 6.5, Microbatch under oil, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.49	α = 90
b = 89.49	β = 90
c = 420.4	γ = 120

Symmetry
Space Group	H 3 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	IMAGE PLATE	MAR scanner 345 mm plate		2011-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54179

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	2.03	30		0.042	37	8.8		41333			11.2

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)
1	2.03	2.14			0.101	18.5	8.3

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	Direct refinement against model PDB	THROUGHOUT	2z90	2.05	30	39234	2092	99.07	0.16871	0.16675	0.20654	RANDOM	10.167

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]
0.25	0.13		0.25		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.977
r_dihedral_angle_4_deg	14.906
r_dihedral_angle_3_deg	12.5
r_dihedral_angle_1_deg	4.333
r_scangle_it	1.488
r_scbond_it	0.871
r_angle_refined_deg	0.838
r_mcangle_it	0.551
r_mcbond_it	0.281
r_chiral_restr	0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.977
r_dihedral_angle_4_deg	14.906
r_dihedral_angle_3_deg	12.5
r_dihedral_angle_1_deg	4.333
r_scangle_it	1.488
r_scbond_it	0.871
r_angle_refined_deg	0.838
r_mcangle_it	0.551
r_mcbond_it	0.281
r_chiral_restr	0.06
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4888
Nucleic Acid Atoms
Solvent Atoms	327
Heterogen Atoms	12

Software

Software
Software Name	Purpose
MAR345dtb	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.