5TJZ

Structure of 4-Hydroxytetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with NADPH and 2,6 Pyridine Dicarboxylic Acid

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	0.1 M Sodium Chloride, 0.1 M Bis-Tris pH 6.5, 1.5 M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.157	α = 90
b = 67.157	β = 90
c = 251.325	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		2014-08-08	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)	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	1.5	30	95.1	0.054	11.4	7.6		52243

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	1.5	1.53	97.8		0.537	0.792		4.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1C3V	1.5	30	49673	2565	95.14	0.1486	0.1476	0.1687	RANDOM	29.958

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]
-0.26	-0.13		-0.26		0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.648
r_dihedral_angle_4_deg	18.114
r_dihedral_angle_3_deg	11.401
r_dihedral_angle_1_deg	5.483
r_scbond_it	2.354
r_angle_refined_deg	2.036
r_mcangle_it	1.718
r_mcbond_it	1.12
r_chiral_restr	0.147
r_bond_refined_d	0.019

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.648
r_dihedral_angle_4_deg	18.114
r_dihedral_angle_3_deg	11.401
r_dihedral_angle_1_deg	5.483
r_scbond_it	2.354
r_angle_refined_deg	2.036
r_mcangle_it	1.718
r_mcbond_it	1.12
r_chiral_restr	0.147
r_bond_refined_d	0.019
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1807
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	127

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
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.