2YXH

Crystal structure of mazG-related protein from Thermotoga maritima

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.4	293	25% PEG3350, 0.2M MgAcetate, 0.1M Tris-HCl, pH8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.829	α = 90
b = 56.788	β = 90
c = 61.615	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	120	CCD	RIGAKU JUPITER 210			M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	0.97905, 0.90000, 0.97945	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	50	99.7	0.073		6.6	18461	18408	-3

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	2.07	98.8		0.258		5.7	1765

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2	20	17330	930	99.74	0.21472	0.21205	0.26312	RANDOM	37.63

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]
-3.66			6.15		-2.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.791
r_dihedral_angle_4_deg	24.428
r_dihedral_angle_3_deg	17.072
r_scangle_it	6.883
r_dihedral_angle_1_deg	6.075
r_scbond_it	4.839
r_mcangle_it	2.558
r_angle_refined_deg	2.186
r_mcbond_it	1.659
r_nbtor_refined	0.331

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.791
r_dihedral_angle_4_deg	24.428
r_dihedral_angle_3_deg	17.072
r_scangle_it	6.883
r_dihedral_angle_1_deg	6.075
r_scbond_it	4.839
r_mcangle_it	2.558
r_angle_refined_deg	2.186
r_mcbond_it	1.659
r_nbtor_refined	0.331
r_symmetry_hbond_refined	0.282
r_nbd_refined	0.264
r_symmetry_vdw_refined	0.217
r_xyhbond_nbd_refined	0.205
r_metal_ion_refined	0.183
r_chiral_restr	0.149
r_bond_refined_d	0.03
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1871
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	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 R01GM133198.