1YL6 | pdb_00001yl6

crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) (crystal form B)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P9L	PDB ENTRY 1P9L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	292	100 mM Tris/HCl, 24 % PEG 3350, 140 mM MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.13	α = 90
b = 89.46	β = 90
c = 77.52	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		2003-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.00	ELETTRA	5.2R

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	2.9	99	98.9	0.061	23.9	31.1	13831	13831	-3	-3	48.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.95	99.8		0.494	4		657

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1P9L	2.9	30	12552	12552	1237	98.9	0.20415	0.20415	0.19883	0.19	0.25689	0.24	RANDOM	59.521

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]
5.16			1.52		-6.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.649
r_dihedral_angle_3_deg	18.89
r_dihedral_angle_4_deg	17.087
r_scangle_it	6.644
r_dihedral_angle_1_deg	6.622
r_scbond_it	3.915
r_angle_refined_deg	1.689
r_mcangle_it	1.367
r_mcbond_it	0.739
r_nbtor_refined	0.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.649
r_dihedral_angle_3_deg	18.89
r_dihedral_angle_4_deg	17.087
r_scangle_it	6.644
r_dihedral_angle_1_deg	6.622
r_scbond_it	3.915
r_angle_refined_deg	1.689
r_mcangle_it	1.367
r_mcbond_it	0.739
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.25
r_nbd_refined	0.241
r_xyhbond_nbd_refined	0.131
r_symmetry_hbond_refined	0.1
r_chiral_restr	0.096
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3622
Nucleic Acid Atoms
Solvent Atoms	2
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
MOLREP	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.