2DUU

Crystal Structure of apo-form of NADP-Dependent Glyceraldehyde-3-Phosphate Dehydrogenase from Synechococcus Sp.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D2I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	gel-tube method	4.8	293	60% saturation of ammonium sulfate, 0.1M citrate buffer, 0.2M potassium sodium tartrate, pH 4.8, gel-tube method, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.4	α = 90
b = 79.8	β = 102.1
c = 207.2	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	ADSC QUANTUM 4		2005-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL12B2	1.0	SPring-8	BL12B2

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	2.9	50	94.4	0.075	4.5	3.7	53808	50999

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	2.9	3	100		0.34	2	3.8	5398

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2D2I	2.9	50	53808	50999	5175		0.217	0.22	0.275	0.27	RANDOM	60.7

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]
-17.83		-4.87	9.57		8.26

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.4
c_angle_deg	1.4
c_improper_angle_d	0.87
c_bond_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14706
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms	30

Software

Software
Software Name	Purpose
EPMR	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.