5C8L

Crystal Structure of the Bdellovibrio bacteriovorus Nucleoside Diphosphate Sugar Hydrolase

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
2.38	48.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.947	α = 90
b = 103.279	β = 90
c = 51.744	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	1.8	50	92.4	0.064	19.1	5.7		35689

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	1.8	1.86	54.4		0.466		3.4	2065

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	1.8	50	33842	1805	92.26	0.1689	0.1667	0.209	RANDOM	28.662

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]
1.39			-1.3		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.151
r_dihedral_angle_4_deg	17.585
r_dihedral_angle_3_deg	13.251
r_dihedral_angle_1_deg	6.382
r_mcangle_it	2.685
r_mcbond_it	1.824
r_mcbond_other	1.814
r_angle_refined_deg	1.497
r_angle_other_deg	0.786
r_chiral_restr	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.151
r_dihedral_angle_4_deg	17.585
r_dihedral_angle_3_deg	13.251
r_dihedral_angle_1_deg	6.382
r_mcangle_it	2.685
r_mcbond_it	1.824
r_mcbond_other	1.814
r_angle_refined_deg	1.497
r_angle_other_deg	0.786
r_chiral_restr	0.096
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2975
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	85

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.