4PT4

Crystal structure Analysis of N terminal region containing the dimerization domain and DNA binding domain of HU protein(Histone like protein-DNA binding) from Mycobacterium tuberculosis [H37Ra]

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P71	PDB ENTRY 1P71

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2	293	3M Sodium formate, 0.1M Tris-Cl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.774	α = 90
b = 53.974	β = 97.01
c = 41.732	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315	mirrors	2007-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.979	NSLS	X29A

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	2.04	50	98.7	0.092	7.5	3.8		10304

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	2.04	2.12	92.9		0.391		3.4	967

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 1P71	2.04	41.42	10468	10291	491	98.32	0.1906	0.1877	0.2492	RANDOM	34.753

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		1.14	-1.82		3.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38
r_dihedral_angle_4_deg	16.813
r_dihedral_angle_3_deg	15.034
r_dihedral_angle_1_deg	5.884
r_mcangle_it	3.154
r_mcbond_it	2.079
r_mcbond_other	2.077
r_angle_refined_deg	1.477
r_angle_other_deg	0.771
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38
r_dihedral_angle_4_deg	16.813
r_dihedral_angle_3_deg	15.034
r_dihedral_angle_1_deg	5.884
r_mcangle_it	3.154
r_mcbond_it	2.079
r_mcbond_other	2.077
r_angle_refined_deg	1.477
r_angle_other_deg	0.771
r_chiral_restr	0.082
r_bond_refined_d	0.011
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	1465
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
DENZO	data reduction

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.