7OL1 | pdb_00007ol1

The X-ray structure of L-threonine dehydrogenase from the common hospital pathogen Clostridium difficile.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LC1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	5 microlitres of enzyme at a concentration of 5 mg/ml and 5 microlitres of 0.2 M lithium sulphate, 0.1 M Tris-HCl pH 8.5, 30 % v/v PEG 4000 (Molecular Dimensions Limited Structure Screen I, condition 35).

Crystal Properties
Matthews coefficient	Solvent content
5.8	78.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.87	α = 90
b = 180.87	β = 90
c = 88.35	γ = 120

Symmetry
Space Group	P 31 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	PIXEL	DECTRIS PILATUS 2M		2012-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.56	63.28	99.5	0.118	0.118	0.125	0.04	0.998	12.2	9.3		53475

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.56	2.7	99.4		1.778	1.778	1.897	0.646	0.526	0.4	8.3

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5lc1	2.6	63.28	47443	2500	97.28	0.2024	0.2004	0.2389	RANDOM	75.367

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]
-2.95	-1.47		-2.95		9.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.911
r_dihedral_angle_4_deg	23.026
r_dihedral_angle_3_deg	20.797
r_dihedral_angle_1_deg	8.637
r_angle_refined_deg	1.79
r_angle_other_deg	1.297
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.911
r_dihedral_angle_4_deg	23.026
r_dihedral_angle_3_deg	20.797
r_dihedral_angle_1_deg	8.637
r_angle_refined_deg	1.79
r_angle_other_deg	1.297
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5030
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	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 R01GM157729.