5TEK | pdb_00005tek

Apo Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Mycobacterium tuberculosis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YL5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2 M Magnesium Chloride, 0.1 M HEPES pH 7.5, 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.569	α = 90
b = 122.607	β = 90
c = 80.846	γ = 90

Symmetry
Space Group	P 21 21 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	MARRESEARCH		2013-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	1	APS	21-ID-G

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	40	99.6	0.061	0.061	13	5.5		40777		-3

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	2.03	99.3		0.655	0.856		4.8

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	1YL5	2.01	40	38724	2023	98.97	0.1932	0.192	0.2	0.2167	0.22	RANDOM	55.381

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]
3.68			-1.4		-2.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.279
r_dihedral_angle_4_deg	23.114
r_dihedral_angle_3_deg	12.898
r_dihedral_angle_1_deg	5.561
r_angle_other_deg	3.745
r_mcangle_it	2.802
r_mcbond_it	1.811
r_mcbond_other	1.81
r_angle_refined_deg	1.558
r_chiral_restr	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.279
r_dihedral_angle_4_deg	23.114
r_dihedral_angle_3_deg	12.898
r_dihedral_angle_1_deg	5.561
r_angle_other_deg	3.745
r_mcangle_it	2.802
r_mcbond_it	1.811
r_mcbond_other	1.81
r_angle_refined_deg	1.558
r_chiral_restr	0.08
r_bond_refined_d	0.012
r_gen_planes_other	0.009
r_gen_planes_refined	0.007
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3639
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	22

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.