3CCG

Crystal structure of predicted HD superfamily hydrolase involved in NAD metabolism (NP_347894.1) from Clostridium acetobutylicum at 1.50 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.9	277	NANODROP, 0.2M Mg formate, 20.0% PEG 3350, 0.001M Spermine tetra-HCl, No Buffer pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.54	α = 90
b = 36.32	β = 125.46
c = 72.6	γ = 90

Symmetry
Space Group	C 1 2 1

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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-02-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97922, 0.97874	SSRL	BL11-1

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	1.5	25.872	98.3	0.038	11.53			30979		-3	17.062

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	1.5	1.55	96.7		0.362	2.1

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	MAD	THROUGHOUT	1.5	25.872	30979	1560	99.56	0.182	0.18	0.217	RANDOM	15.356

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]
-0.75		-1	0.29		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.877
r_dihedral_angle_4_deg	13.723
r_dihedral_angle_3_deg	11.479
r_scangle_it	6.33
r_scbond_it	4.39
r_dihedral_angle_1_deg	3.972
r_mcangle_it	2.848
r_mcbond_it	1.826
r_angle_refined_deg	1.563
r_angle_other_deg	1.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.877
r_dihedral_angle_4_deg	13.723
r_dihedral_angle_3_deg	11.479
r_scangle_it	6.33
r_scbond_it	4.39
r_dihedral_angle_1_deg	3.972
r_mcangle_it	2.848
r_mcbond_it	1.826
r_angle_refined_deg	1.563
r_angle_other_deg	1.065
r_mcbond_other	0.527
r_chiral_restr	0.078
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1472
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	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.