2TDT | pdb_00002tdt

COMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH 2-AMINOPIMELATE AND COENZYME A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TDT	PDB ENTRY 1TDT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.4		10-13 % (W/V) POLYETHYLENE GLYCOL 4000 94 MM MES, PH 6.4 94 MM AMMONIUM SULFATE 4.7 (V/V) 2-PROPANOL 16 MM (D,L)-2-AMINOPIMELATE 2.5 MM COENZYME A

Crystal Properties
Matthews coefficient	Solvent content
2.15	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.71	α = 90
b = 95.71	β = 90
c = 72.79	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	AREA DETECTOR	SIEMENS		1997-08-24	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2		98.1	0.047	0.047	22.7	2.7		44276

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.1	98.1		0.215	0.215	3.4	1.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1TDT	2	99	16215	16215	813	98.1	0.171	0.171	0.169	0.24	SHELLS

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
t_dihedral_angle_d	23.9
t_it	5.22
t_angle_deg	1.94
t_nbd	0.025
t_bond_d	0.023
t_gen_planes	0.017
t_trig_c_planes	0.011
t_incorr_chiral_ct
t_pseud_angle

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2075
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	60

Software

Software
Software Name	Purpose
X-PLOR	model building
TNT	refinement
X-PLOR	refinement
XDS	data reduction
XSCALE	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.