5C7T

Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase in complex with ADP-ribose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	1.75-2.0 M ammonium sulfate, 0.1 M HEPES pH 7.0, and 0-0.5% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.594	α = 90
b = 103.402	β = 90
c = 51.623	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	93	CCD	RIGAKU SATURN 944+		2010-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ DW	1.541

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	2.06	50	95	0.095	11.9	5.4		24431

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	2.06	2.13	68.9		0.525		2.1	1726

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	FOURIER SYNTHESIS	THROUGHOUT	5c7Q	2.06	26.8	23061	1256	95.08	0.1845	0.1812	0.245	RANDOM	31.191

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]
1.3			-0.58		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.768
r_dihedral_angle_4_deg	21.497
r_dihedral_angle_3_deg	14.341
r_dihedral_angle_1_deg	6.627
r_mcangle_it	3.18
r_mcbond_it	2.204
r_mcbond_other	2.202
r_angle_refined_deg	1.886
r_angle_other_deg	0.832
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.768
r_dihedral_angle_4_deg	21.497
r_dihedral_angle_3_deg	14.341
r_dihedral_angle_1_deg	6.627
r_mcangle_it	3.18
r_mcbond_it	2.204
r_mcbond_other	2.202
r_angle_refined_deg	1.886
r_angle_other_deg	0.832
r_chiral_restr	0.107
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2975
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	169

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
REFMAC	refinement
REFMAC	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.