Experiment: 1DXY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GDH	BACKBONE AND C-BETA ATOMS OF D-GLYCERATE DEHYDROGENASE (PDB ENTRY 1GDH)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	277	1.9 M AMMONIUM SULFATE, 50 MM CITRATE/PHOSPHATE BUFFER, 30 MM NAD+, 60 MM 4-METHYL-2-OXOPENTANOATE, PH 7.0, 277 K; ENZYME CONCENTRATION 10 MG/ML.

Crystal Properties
Matthews coefficient	Solvent content
4.4	72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.1	α = 90
b = 134.1	β = 90
c = 125.1	γ = 120

Symmetry
Space Group	P 63 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	277	IMAGE PLATE	MAR scanner 300 mm plate	MIRROR OPTICS	1994-08-01	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6		MPG/DESY, HAMBURG	BW6

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.86	12.1	96.5	0.089	22.2	5.8		53838

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	2	86.9		0.48	2.8	4.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	BACKBONE AND C-BETA ATOMS OF D-GLYCERATE DEHYDROGENASE (PDB ENTRY 1GDH)	1.86	12.1	53838		96.5	0.196	0.196	0.18	0.217	31.02

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	23.12
x_angle_deg	1.73
x_improper_angle_d	1.25
x_bond_d	0.009
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2580
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	63

Software

Software
Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
ROTAVATA	data scaling
X-PLOR	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.