1ZH8 | pdb_00001zh8

Crystal structure of Oxidoreductase (TM0312) from Thermotoga maritima at 2.50 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	7.5	277	8.0% Ethylene-Glycol, 10.0% PEG-8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.68	53.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.849	α = 90
b = 63.088	β = 104.88
c = 101.172	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	100	CCD	MARMOSAIC 325 mm CCD		2005-03-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97929	SSRL	BL9-2

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	2.5	28.96	99.9	0.085	0.085	6.9	3.7		27566

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	2.5	2.56	100		0.374	0.374	2	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.5	28	26222	1382	99.7	0.196	0.19618	0.194	0.1955	0.237	0.2287	RANDOM	37.297

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]
1.73		1.08	-0.14		-1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.919
r_dihedral_angle_4_deg	19.759
r_dihedral_angle_3_deg	15.032
r_scangle_it	6.619
r_dihedral_angle_1_deg	6.079
r_scbond_it	4.759
r_mcangle_it	2.376
r_angle_refined_deg	1.389
r_mcbond_it	1.296
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.919
r_dihedral_angle_4_deg	19.759
r_dihedral_angle_3_deg	15.032
r_scangle_it	6.619
r_dihedral_angle_1_deg	6.079
r_scbond_it	4.759
r_mcangle_it	2.376
r_angle_refined_deg	1.389
r_mcbond_it	1.296
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.277
r_metal_ion_refined	0.21
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.148
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5026
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	118

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	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.