3RVD

Crystal structure of the binary complex, obtained by soaking, of photosyntetic a4 glyceraldehyde 3-phosphate dehydrogenase (gapdh) with cp12-2, both from arabidopsis thaliana.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K2B	PDB ENTRY 3K2B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.4 M ammonium sulphate, 0.1 M sodium citrate, 1 mM NAD, 3.125 mg/ml CP12 for soaking experiments, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.183	α = 90
b = 188.75	β = 90
c = 312.17	γ = 90

Symmetry
Space Group	I 2 2 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	ADSC QUANTUM 210		2006-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

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	2.7	95.3	96.6	0.098	0.098	16.3	11.3	119322	118509	3	-3	27.5

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	2.7	2.8	84		0.587	0.587	2.1	7.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3K2B	2.7	94.61	119322	118509	11850	95.7	0.247	0.247	0.24	0.318	0.26	RANDOM	63.5

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]
31.48			-11.8		-19.68

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.6
c_scangle_it	2.37
c_mcangle_it	1.93
c_scbond_it	1.49
c_angle_deg	1.4
c_mcbond_it	1.11
c_improper_angle_d	0.93
c_bond_d	0.009
c_bond_d_na
c_bond_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26538
Nucleic Acid Atoms
Solvent Atoms	556
Heterogen Atoms	580

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	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.