3AFQ

Crystal structure of the single-stranded DNA binding protein from Mycobacterium leprae (Form II)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AFP	PDB ENTRY 3AFP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.5	298	0.1M HEPES, 3M NaCl, pH 7.5, microbatch, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.486	α = 90
b = 102.486	β = 90
c = 120.762	γ = 120

Symmetry
Space Group	P 32 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	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2006-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	30	99.7	0.059	15.3	2.4		18449			75.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9			0.517	2		1810

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3AFP	2.8	30	17563	916	99.72	0.21246	0.21129	0.23545	RANDOM	71.644

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]
3.41			3.41		-6.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.945
r_dihedral_angle_3_deg	18.189
r_dihedral_angle_4_deg	16.866
r_scangle_it	7.303
r_dihedral_angle_1_deg	5.888
r_mcangle_it	4.464
r_scbond_it	4.106
r_mcbond_it	2.663
r_angle_refined_deg	1.462
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.945
r_dihedral_angle_3_deg	18.189
r_dihedral_angle_4_deg	16.866
r_scangle_it	7.303
r_dihedral_angle_1_deg	5.888
r_mcangle_it	4.464
r_scbond_it	4.106
r_mcbond_it	2.663
r_angle_refined_deg	1.462
r_chiral_restr	0.095
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3165
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASES	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	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 R01GM133198.