1Z9F | pdb_00001z9f

Crystal structure of single stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	8	293	25.0% MPD, 0.1M TRIS pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.589	α = 90
b = 83.406	β = 90
c = 86.431	γ = 90

Symmetry
Space Group	F 2 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	CCD	ADSC QUANTUM 4		2003-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3		ALS	5.0.3

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	2.3	47.22	68	0.062	7.5	4.3		4323

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	2.3	2.36		28.6	0.324	2.3	2.3

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 (All)	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	1sru	2.3	47.22	3902	420	68.41	0.231	0.23054	0.223	0.23	0.3	0.3	RANDOM	77.965

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]
-1.1			1.84		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.089
r_dihedral_angle_4_deg	18.607
r_dihedral_angle_3_deg	17.262
r_dihedral_angle_1_deg	8.732
r_scangle_it	2.125
r_angle_refined_deg	1.492
r_scbond_it	1.361
r_mcangle_it	0.838
r_angle_other_deg	0.827
r_mcbond_it	0.514
r_symmetry_vdw_refined	0.215
r_xyhbond_nbd_refined	0.205
r_nbd_refined	0.199
r_nbd_other	0.192
r_symmetry_vdw_other	0.185
r_nbtor_refined	0.18
r_symmetry_hbond_refined	0.143
r_mcbond_other	0.099
r_chiral_restr	0.085
r_nbtor_other	0.084
r_xyhbond_nbd_other	0.019
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	724
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing