5GQO | pdb_00005gqo

Structure of the second Single Stranded DNA Binding protein (SSBb) from Mycobacterium smegmatis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.5	298	0.2M calcium chloride dihydrate, 0.1M HEPES pH 7.5, 7.5 % (v/v) PEG 400, 3% (w/v) 1,5-diaminopentane dihydrochloride

Crystal Properties
Matthews coefficient	Solvent content
2.22	39.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.61	α = 90
b = 73.61	β = 90
c = 216.21	γ = 120

Symmetry
Space Group	P 65 2 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	mirrors	2015-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5419

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	CC (Half)	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	2.5	43.24	99.9	0.093	0.093	0.999	16.4	9.9		12839		2	54.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	100		0.1	0.671	2.3	9.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3EIV	2.5	43.24	12140	624	99.91	0.21334	0.21123	0.22	0.25627	0.26	RANDOM	54.635

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]
0.08	0.04		0.08		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.482
r_dihedral_angle_4_deg	22.772
r_dihedral_angle_3_deg	19.685
r_long_range_B_other	11.132
r_long_range_B_refined	11.123
r_scangle_other	8.291
r_mcangle_other	7.764
r_mcangle_it	7.761
r_dihedral_angle_1_deg	7.358
r_scbond_it	5.555
r_scbond_other	5.552
r_mcbond_it	5.211
r_mcbond_other	5.183
r_angle_refined_deg	1.775
r_angle_other_deg	1.163
r_chiral_restr	0.105
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.005
r_gen_planes_other	0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1493
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing