Experiment: 2EJV

Crystal structure of threonine 3-dehydrogenase complexed with NAD+

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DQ4	PDB ENTRY 2DQ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.8M Sodium Acetate, 0.1M Mes pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.87	74.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.758	α = 90
b = 135.758	β = 90
c = 268.593	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	IMAGE PLATE	RIGAKU RAXIS V		2003-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.0	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.55	50	99.5				48510			55.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2DQ4	2.55	19.99	48074	4849	99.5	0.207	0.207	0.21	0.236	0.2387	RANDOM	49.6

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]
2.39	4.44		2.39		-4.77

RMS Deviations
Key	Refinement Restraint Deviation
c_scbond_it	30.95
c_scangle_it	28.18
c_dihedral_angle_d	24.3
c_mcangle_it	1.75
c_angle_deg	1.5
c_mcbond_it	1.08
c_improper_angle_d	0.92
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5129
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	92

Software

Software
Software Name	Purpose
CNS	refinement
CrystalClear	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing