4Z0H

X-ray structure of cytoplasmic glyceraldehyde-3-phosphate dehydrogenase (GapC1) complexed with NAD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	3.0-3.5 M ammonium sulphate, 0.1 M Na-Hepes.

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.849	α = 90
b = 76.849	β = 90
c = 406.626	γ = 120

Symmetry
Space Group	P 61 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 315r		2011-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.939	ESRF	ID14-4

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	2.18	101.66	99.7	0.129	0.129	8.4	8.1		38786	3	-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	2.18	2.3	98.4		0.454	2.2	6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3K2B	2.3	67.77	31304	1653	99.66	0.2508	0.2493	0.2777	RANDOM	47.534

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]
3.46	1.73		3.46		-5.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.573
r_dihedral_angle_3_deg	22.591
r_dihedral_angle_4_deg	22.105
r_dihedral_angle_1_deg	6.873
r_scangle_it	3.787
r_scbond_it	2.4
r_angle_refined_deg	1.94
r_mcangle_it	1.914
r_mcbond_it	1.088
r_chiral_restr	0.118

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.573
r_dihedral_angle_3_deg	22.591
r_dihedral_angle_4_deg	22.105
r_dihedral_angle_1_deg	6.873
r_scangle_it	3.787
r_scbond_it	2.4
r_angle_refined_deg	1.94
r_mcangle_it	1.914
r_mcbond_it	1.088
r_chiral_restr	0.118
r_bond_refined_d	0.022
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5127
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	123

Software

Software
Software Name	Purpose
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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 R01GM133198.