2Q16 | pdb_00002q16

Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	25% PEG 4K, 200 mM Ammonium Sulfate, 100 mM Sodium Acetate, 2% iso-Propanol, 20 mM Calcium Chloride, 10mM ITP, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.646	α = 90
b = 120.646	β = 90
c = 66.562	γ = 90

Symmetry
Space Group	P 4 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	mirrors	2006-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97942	APS	19-ID

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	1.95	500	99.96	0.089	39.9	19.4	36421	36385			24.8

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	1.95	2	100		0.551	5.5	17.7	2359

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	THROUGHOUT	1.95	26.98	36421	34514	1813	99.93	0.17278	0.17278	0.17086	0.17	0.20829	0.21	RANDOM	29.725

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]
-0.01			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.998
r_dihedral_angle_4_deg	20.06
r_dihedral_angle_3_deg	13.263
r_dihedral_angle_1_deg	10.601
r_scangle_it	4.087
r_scbond_it	2.518
r_angle_refined_deg	1.678
r_mcangle_it	1.502
r_mcbond_it	0.833
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.998
r_dihedral_angle_4_deg	20.06
r_dihedral_angle_3_deg	13.263
r_dihedral_angle_1_deg	10.601
r_scangle_it	4.087
r_scbond_it	2.518
r_angle_refined_deg	1.678
r_mcangle_it	1.502
r_mcbond_it	0.833
r_nbtor_refined	0.304
r_symmetry_hbond_refined	0.218
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.208
r_metal_ion_refined	0.191
r_symmetry_vdw_refined	0.152
r_chiral_restr	0.123
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2922
Nucleic Acid Atoms
Solvent Atoms	410
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHARP	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.