Experiment: 2JKV

Structure of human Phosphogluconate Dehydrogenase in complex with NADPH at 2.53A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PGP	PDB ENTRIES 1PGP, 1PGN
experimental model	PDB	1PGN	PDB ENTRIES 1PGP, 1PGN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.20M NA2SO4, 20.0% PEG 3350, 10.0% ETGLY

Crystal Properties
Matthews coefficient	Solvent content
2.93	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.643	α = 90
b = 204.714	β = 90.65
c = 170.319	γ = 90

Symmetry
Space Group	P 1 21 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	MARRESEARCH	MIRRORS	2008-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	2.53	37	97.9	0.14	7.8	3.7		128646

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	2.53	2.67	87.1		0.57	2.1	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRIES 1PGP, 1PGN	2.532	36.899	0.01	118499	1982	92.18	0.1566	0.1558	0.1555	0.2069	0.203

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]
1.7989		0.4807	-3.2451		1.4461

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.042
f_angle_d	1.069
f_chiral_restr	0.074
f_bond_d	0.008
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	22103
Nucleic Acid Atoms
Solvent Atoms	1405
Heterogen Atoms	311

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing