1SJ5

Crystal structure of a duf151 family protein (tm0160) from thermotoga maritima at 2.8 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O5Y	PDB ENTRY 1O5Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.9		pH 6.90

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.001	α = 90
b = 52.136	β = 97.64
c = 73.33	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	90	IMAGE PLATE	RIGAKU RAXIS IV			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300

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	72.55	98.2	0.079	12			8172

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	98.9		0.652	3.1

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1O5Y	2.8	72.55	7762	349	98.2	0.21858	0.21571	0.23	0.27555	0.25	RANDOM	22.388

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]
-3.52		-1.26	1.55		1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.853
r_scangle_it	4.847
r_scbond_it	3.309
r_angle_refined_deg	1.635
r_mcangle_it	1.061
r_angle_other_deg	0.878
r_mcbond_it	0.441
r_symmetry_hbond_refined	0.323
r_symmetry_vdw_other	0.28
r_nbd_refined	0.232
r_nbd_other	0.231
r_symmetry_vdw_refined	0.211
r_xyhbond_nbd_refined	0.159
r_nbtor_other	0.088
r_chiral_restr	0.081
r_bond_refined_d	0.017
r_gen_planes_other	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2173
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
CCP4	phasing