Experiment: 3PYM

Structure of GAPDH 3 from S.cerevisiae at 2.0 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GD1	PDB ENTRY 1GD1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	10.5-15.5% PEG, 50mM NaAc, 1mm DTT, 1mm NAD, pH 7.0, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.834	α = 90
b = 131.052	β = 90
c = 96.685	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		CCD	ADSC QUANTUM 4r		2004-01-04

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9340	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	48.34	99.9	0.094	0.091		14.7	52637	52575	1	1

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-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	MOLECULAR REPLACEMENT	PDB ENTRY 1GD1	2	44.615	57581	52308	5273	99.29	0.1516	0.1516	0.1473	0.1475	0.1888	0.1912	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]
2.3726			-1.7782		-0.5944

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.227
f_angle_d	1.517
f_chiral_restr	0.093
f_bond_d	0.014
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5020
Nucleic Acid Atoms
Solvent Atoms	492
Heterogen Atoms	105

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling