1KY8 | pdb_00001ky8

Crystal Structure of the Non-phosphorylating glyceraldehyde-3-phosphate Dehydrogenase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	sodium formate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 20K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 185.2	α = 90
b = 185.2	β = 90
c = 132.1	γ = 120

Symmetry
Space Group	P 62 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	IMAGE PLATE	MARRESEARCH		1999-04-04	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	MARRESEARCH		1999-01-01	M	MAD
3	1	x-ray	100	IMAGE PLATE	MARRESEARCH		1999-01-01	M	MAD
4	1	x-ray	100	IMAGE PLATE	MARRESEARCH		1999-01-01	M	MAD
1,2,3,4	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.8469	EMBL/DESY, HAMBURG	BW7B
2	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.9796	EMBL/DESY, HAMBURG	BW7A
3	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.9792	EMBL/DESY, HAMBURG	BW7A
4	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.9724	EMBL/DESY, HAMBURG	BW7A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
1,2,3,4	2.4	30	99.1			52004	52004

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2,3,4	2.4	2.5	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	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	MAD	2.4	30	52004	52004	2626		0.208	0.2	0.242	0.24	random

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_angle_deg	1.48
x_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3772
Nucleic Acid Atoms
Solvent Atoms	386
Heterogen Atoms	49

Software

Software
Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
SOLVE	phasing
SHELX	model building
X-PLOR	refinement
SHELX	phasing

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.