1Z77 | pdb_00001z77

Crystal structure of transcriptional regulator protein from Thermotoga maritima.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	0.05M Na citrate, 30% w/v PEG 2K MME, 0.1M KSCN, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.043	α = 90
b = 65.684	β = 90
c = 55.694	γ = 90

Symmetry
Space Group	P 21 21 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 315		2005-02-11	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	SBC-3		2005-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.91932	APS	19-ID
2	SYNCHROTRON	APS BEAMLINE 19-BM	0.97932	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.95	50	98.5	0.07	0.07	24.84	8.1		15569		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.95	2.02	100		0.539	0.471	3.3	8.6	1531

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD/SAD	THROUGHOUT	2	50	14438	13472	715	98.26	0.23129	0.23129	0.22944	0.25	0.26671	0.28	RANDOM	37.765

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]
-2.29			1.53		0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.921
r_dihedral_angle_4_deg	16.246
r_dihedral_angle_3_deg	13.892
r_dihedral_angle_1_deg	5.153
r_scangle_it	4.916
r_scbond_it	3.631
r_mcangle_it	1.888
r_angle_refined_deg	1.667
r_mcbond_it	1.454
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.921
r_dihedral_angle_4_deg	16.246
r_dihedral_angle_3_deg	13.892
r_dihedral_angle_1_deg	5.153
r_scangle_it	4.916
r_scbond_it	3.631
r_mcangle_it	1.888
r_angle_refined_deg	1.667
r_mcbond_it	1.454
r_nbtor_refined	0.31
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.194
r_symmetry_hbond_refined	0.176
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.112
r_bond_refined_d	0.022
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1596
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
O	model building
Coot	model building
CCP4	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.