2DJW | pdb_00002djw

Crystal structure of TTHA0845 from Thermus thermophilus HB8

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		This protein model solved by MAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	8.35mg/mL Protein, 2% PEG3350, 20mM Zn(OAc)2, 10mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.883	α = 90
b = 95.883	β = 90
c = 119.01	γ = 120

Symmetry
Space Group	P 32

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	RIGAKU JUPITER 210	mirrors	2004-11-08	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	RIGAKU JUPITER 210		2004-11-08	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.0000	SPring-8	BL26B2
2	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.28220, 1.28280, 1.26000	SPring-8	BL26B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.4	30	99.9	0.04	37.4	6.3		47780			61.252

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.4	2.49	100		0.304	6.6	6.4	4755

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MAD, MOLECULAR REPLACEMENT	THROUGHOUT	This protein model solved by MAD	2.4	30	45287	45287	2415	99.75	0.25198	0.25198	0.24977	0.24	0.29351	0.28	RANDOM	52.23

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]
0.11	0.06		0.11		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.41
r_dihedral_angle_4_deg	20.368
r_dihedral_angle_3_deg	18.24
r_dihedral_angle_1_deg	6.773
r_scangle_it	2.665
r_scbond_it	1.64
r_angle_refined_deg	1.394
r_mcangle_it	1.33
r_mcbond_it	0.742
r_symmetry_vdw_refined	0.382
r_metal_ion_refined	0.345
r_nbtor_refined	0.304
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.095
r_symmetry_hbond_refined	0.095
r_symmetry_metal_ion_refined	0.06
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_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	6219
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing