3RHD

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase GapN from Methanocaldococcus jannaschii DSM 2661 complexed with NADP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	35% MPD, 0.1M acetate, 4.5, 2 mM NADPH, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.243	α = 90
b = 77.384	β = 118.29
c = 167.389	γ = 90

Symmetry
Space Group	C 1 2 1

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 315		2011-02-11		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9791	NSLS	X29A

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	2.2	50	99.7	0.116	6.6	5.4		93993

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	2.2	2.24	96.5			5	4547

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	3PQA	2.2	19.96	93586	4688	99.59	0.1823	0.1794	0.2385	RANDOM	27.9527

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]
0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.078
r_dihedral_angle_3_deg	15.649
r_dihedral_angle_4_deg	15.35
r_scbond_it	8.449
r_dihedral_angle_1_deg	6.078
r_mcangle_it	3.375
r_angle_refined_deg	1.264
r_scangle_it	0.829
r_mcbond_it	0.702
r_chiral_restr	0.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.078
r_dihedral_angle_3_deg	15.649
r_dihedral_angle_4_deg	15.35
r_scbond_it	8.449
r_dihedral_angle_1_deg	6.078
r_mcangle_it	3.375
r_angle_refined_deg	1.264
r_scangle_it	0.829
r_mcbond_it	0.702
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14132
Nucleic Acid Atoms
Solvent Atoms	610
Heterogen Atoms	124

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	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 R01GM157729.