7R4W | pdb_00007r4w

Single stranded DNA binding protein SSB M5 from Fervidobacterium gondwanense

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VW9	2vW9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		293	1 M Diammonium phosphate, 0.1 M sodium acetate pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.39	α = 90
b = 62.39	β = 90
c = 172.38	γ = 90

Symmetry
Space Group	I 41 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	PIXEL	DECTRIS EIGER2 X 16M		2020-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.3	43.13	99.4	0.131	0.134	0.027	0.999	17.6	25.8		7947

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	99.5		5.5	5.603	1.061	0.521		27.1

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	2vW9	2.3	43.13	7538	391	99.41	0.1902	0.187	0.1937	0.2548	0.2598	RANDOM	90.814

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]
2.53			2.53		-5.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.342
r_dihedral_angle_4_deg	19.169
r_dihedral_angle_3_deg	17.807
r_dihedral_angle_1_deg	8.385
r_angle_refined_deg	2.091
r_angle_other_deg	1.392
r_chiral_restr	0.08
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	804
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	13

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MrBUMP	phasing