3LMM

Crystal Structure of the DIP2311 protein from Corynebacterium diphtheriae, Northeast Structural Genomics Consortium Target CdR35

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6	291	Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1M Na acetate (pH 4.6), 1M 1,6-hexanediol, and 10 mM CoCl2, Microbatch, under oil, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
4.31	71.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.306	α = 90
b = 102.03	β = 116
c = 164.515	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 4	mirrors	2009-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.97901	NSLS	X4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3	30	99.7	0.13	0.102	9.8	3.4	172553	172016			38.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3	3.11	99.4		0.525	0.441	2.2	3.3	17096

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	3	19.99	2	2	171771	139822	6959	81.4	0.187	0.185	0.183	0.231	RANDOM	43.8

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]
-12.58		2.87	3.38		9.2

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23
c_angle_deg	1.2
c_improper_angle_d	0.86
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16007
Nucleic Acid Atoms
Solvent Atoms	391
Heterogen Atoms	10

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SHELX	data scaling
SOLVE	phasing
RESOLVE	phasing
SHELX	phasing
REFMAC	refinement

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.