1VK6

Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		277	12% MPD, 0.08M HEPES, 0.02M HEPES_Na , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.13	69.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.319	α = 90
b = 127.319	β = 90
c = 108.405	γ = 120

Symmetry
Space Group	P 65 2 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		2003-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	63.66	100	0.068	13.9	7.4		26842			53.64

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	100		0.588	2.3	4.7	3836

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.2	63.66	25436	1371	99.87	0.18831	0.18668	0.21955	RANDOM	68.881

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]
1.85	0.92		1.85		-2.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.71
r_dihedral_angle_4_deg	15.135
r_dihedral_angle_3_deg	14.851
r_scangle_it	7.928
r_scbond_it	6.251
r_dihedral_angle_1_deg	5.824
r_mcangle_it	3.466
r_mcbond_it	2.452
r_angle_refined_deg	1.509
r_symmetry_vdw_refined	0.201

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.71
r_dihedral_angle_4_deg	15.135
r_dihedral_angle_3_deg	14.851
r_scangle_it	7.928
r_scbond_it	6.251
r_dihedral_angle_1_deg	5.824
r_mcangle_it	3.466
r_mcbond_it	2.452
r_angle_refined_deg	1.509
r_symmetry_vdw_refined	0.201
r_nbd_refined	0.195
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.102
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2053
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.