5TJY | pdb_00005tjy

Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with 2,6 Pyridine Dicarboxylic Acid and NADH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1C3V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	50 mM Ammonium Sulfate, 50 mM Bis-Tris pH 6.5, 30% v/v Pentaerythritol ethoxylate (15/4 EO/OH)

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.421	α = 90
b = 66.421	β = 90
c = 249.363	γ = 120

Symmetry
Space Group	P 62 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	CCD	ADSC QUANTUM 315r		2014-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.4	40	99.9	0.102	0.105	0.023	7.3	20.5		13744

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44	100		0.813	0.947		20.7

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	1C3V	2.4	40	12914	663	99.52	0.148	0.1456	0.16	0.1949	0.21	RANDOM	43.662

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]
0.99	0.5		0.99		-3.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.123
r_dihedral_angle_4_deg	20.04
r_dihedral_angle_3_deg	12.363
r_dihedral_angle_1_deg	6.331
r_mcangle_it	4.312
r_mcbond_other	3.211
r_mcbond_it	3.209
r_angle_refined_deg	1.914
r_angle_other_deg	1.012
r_chiral_restr	0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.123
r_dihedral_angle_4_deg	20.04
r_dihedral_angle_3_deg	12.363
r_dihedral_angle_1_deg	6.331
r_mcangle_it	4.312
r_mcbond_other	3.211
r_mcbond_it	3.209
r_angle_refined_deg	1.914
r_angle_other_deg	1.012
r_chiral_restr	0.101
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1807
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	108

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	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.