1YL7 | pdb_00001yl7

the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	292	100 mM Tris/HCl, 26 % PEG 3350, 140 mM MgCl2 + 3 mM NADH in the protein solution, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 238.6	α = 90
b = 67.52	β = 117.08
c = 154.49	γ = 90

Symmetry
Space Group	C 1 2 1

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		2003-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8042	EMBL/DESY, HAMBURG	X13

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	2.34	99	86.6	0.091	18.7	18.9	80382	80382	-3	-3	36.5

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	2.34	2.38	76.6		0.301	3.3		3491

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 (MONOMER)	2.34	30	77923	77923	2428	86.57	0.18307	0.18307	0.18134	0.18	0.2381	0.23	RANDOM	41.528

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]
0.24		-1.04	-0.43		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.266
r_dihedral_angle_4_deg	21.863
r_dihedral_angle_3_deg	15.971
r_dihedral_angle_1_deg	5.597
r_scangle_it	5.141
r_scbond_it	3.313
r_angle_refined_deg	1.384
r_mcangle_it	1.202
r_mcbond_it	0.642
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.266
r_dihedral_angle_4_deg	21.863
r_dihedral_angle_3_deg	15.971
r_dihedral_angle_1_deg	5.597
r_scangle_it	5.141
r_scbond_it	3.313
r_angle_refined_deg	1.384
r_mcangle_it	1.202
r_mcbond_it	0.642
r_nbtor_refined	0.301
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.137
r_symmetry_vdw_refined	0.13
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14428
Nucleic Acid Atoms
Solvent Atoms	356
Heterogen Atoms	358

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.