5IE9

Crystal structure of the Bacillus-conserved MazG protein, a nucleotide pyrophosphohydrolase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GTA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1mM sodium cacodylate pH 6.5, 1M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
4.78	74.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.578	α = 90
b = 90.578	β = 90
c = 97.056	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	83	CCD	ADSC QUANTUM 1		2014-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.9798	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.77	30	98.7		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.87	89.4		2	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2GTA	2.8	30	20632	1059	98.86	0.2232	0.2217	0.2537	RANDOM	46

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]
-0.22	-0.11		-0.22		0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.257
r_dihedral_angle_3_deg	20.603
r_dihedral_angle_4_deg	17.319
r_dihedral_angle_1_deg	4.738
r_mcangle_it	1.677
r_scbond_it	1.378
r_angle_refined_deg	1.318
r_mcbond_it	0.955
r_chiral_restr	0.086
r_bond_refined_d	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.257
r_dihedral_angle_3_deg	20.603
r_dihedral_angle_4_deg	17.319
r_dihedral_angle_1_deg	4.738
r_mcangle_it	1.677
r_scbond_it	1.378
r_angle_refined_deg	1.318
r_mcbond_it	0.955
r_chiral_restr	0.086
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2948
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	4

Software

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