3PG5 | pdb_00003pg5

Crystal structure of protein DIP2308 from Corynebacterium diphtheriae, Northeast Structural Genomics Consortium Target CdR78

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	micro batch under oil	9	277	Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 0.1 M TAPS (pH 9), 40% PEG400, and 0.1 M magnesium nitrate, micro batch under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 199.963	α = 90
b = 199.963	β = 90
c = 106.58	γ = 90

Symmetry
Space Group	P 4 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	100	CCD	MAR CCD 165 mm	mirrors	2010-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.97908	NSLS	X4C

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	3.3	30	100	0.23	0.187	13.47	13.6	62028	62028			55.2

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)
1	3.3	3.42	100		0.814	0.738	2.56	11	6231

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	3.3	20	1	1	61882	54766	5408	88.5	0.19	0.187	0.187	0.2044	0.235	0.2508	RANDOM	56.6

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]
-5.68			-5.68		11.35

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.3
c_angle_deg	1.1
c_improper_angle_d	0.84
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9592
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
SHELX	model building
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing