2YYY | pdb_00002yyy

Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CF2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	oil-batch	8.5	293	0.2M magnesium chloride hexahydrate, 0.08M tris hydrochloride, pH 8.5, 24%(w/v) PEG4000, 20%(v/v) glycerol anhydrous, oil-batch, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.398	α = 90
b = 152.04	β = 90
c = 118.552	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	1.117	SRS	PX10.1

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	1.85	50	97.1	0.066		4.5	64389	62507	-3

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)
	1.85	1.92	78.1		0.238		2.9	4944

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1CF2	1.85	20	59323	3146	97.1	0.17069	0.16923	0.19795	RANDOM	18.797

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]
0.86			0.04		-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.116
r_scangle_it	3.886
r_scbond_it	2.418
r_angle_refined_deg	1.507
r_mcangle_it	1.296
r_mcbond_it	0.724
r_symmetry_hbond_refined	0.221
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.116
r_scangle_it	3.886
r_scbond_it	2.418
r_angle_refined_deg	1.507
r_mcangle_it	1.296
r_mcbond_it	0.724
r_symmetry_hbond_refined	0.221
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5328
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	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.