4JZT | pdb_00004jzt

Crystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH (E68A mutant) bound to GTP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		STRUCTURE OF BSRPPH E68A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.3	293	1.9 M ammonium sulfate, 0.1 M Tris pH 8.3, 10 mM TCEP, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.652	α = 90
b = 117.652	β = 90
c = 55.605	γ = 120

Symmetry
Space Group	P 63

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 210		2011-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.93340	ESRF	ID14-1

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	2.9	48.81	100	0.071	26.3	7.5	9913	9913	-3	-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	2.9	3.06	100		0.692	2.5	7.5	1422

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	STRUCTURE OF BSRPPH E68A	2.9	48.81	9904	476	100	0.2151	0.2136	0.22	0.2451	0.26	RANDOM	82.0431

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]
-4.6362			-4.6362		9.2724

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	20.36
t_omega_torsion	2.06
t_angle_deg	0.94
t_bond_d	0.007
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2606
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	32

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
BUSTER	refinement

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.