4L6W | pdb_00004l6w

Carboxyltransferase subunit (AccD6) of Mycobacterium tuberculosis acetyl-CoA carboxylase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BZR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	27% (w/v) PEG 3350, 0.3 M ammonium sulphate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.942	α = 90
b = 90.311	β = 90
c = 154.563	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	25 Hz, 450 micron sensor thickness	2012-11-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	1.2395	PETRA III, EMBL c/o DESY	P14 (MX2)

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	1.947	76.942	99.85	0.038	34.4	12.88	79503	79385		-3	36.4

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	1.95	2.06	98.59		0.49	5.14	12.9	12489

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	2BZR	1.95	68.97	75286	75286	3977	99.65	0.17721	0.17721	0.17383	0.18	0.24356	0.24	RANDOM	44.222

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]
0.33			0.35		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.005
r_sphericity_bonded	26.704
r_sphericity_free	23.818
r_dihedral_angle_4_deg	19.705
r_dihedral_angle_3_deg	15.618
r_rigid_bond_restr	7.444
r_dihedral_angle_1_deg	6.288
r_angle_refined_deg	1.846
r_chiral_restr	0.13
r_bond_refined_d	0.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.005
r_sphericity_bonded	26.704
r_sphericity_free	23.818
r_dihedral_angle_4_deg	19.705
r_dihedral_angle_3_deg	15.618
r_rigid_bond_restr	7.444
r_dihedral_angle_1_deg	6.288
r_angle_refined_deg	1.846
r_chiral_restr	0.13
r_bond_refined_d	0.017
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6141
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

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.