4Q0G | pdb_00004q0g

Crystal structure of beta subunit of acyl-CoA carboxylase AccD1 from Mycobacterium tuberculosis

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3U9R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.1 M sodium HEPES pH 7.5 and 30% PEG300, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.88	68.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.571	α = 90
b = 221.253	β = 90
c = 167.835	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	RAYONIX MX300HE	vertical focusing mirror: ultra-low expansion titanium silicate flat mirror with Pt, uncoated, and Pd strips.	2011-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

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	2.3	48.81	99.7	0.157	12.93	5.8	116259	115910		-3

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	2.3	2.38	100		0.817	2.66	5.7	11512

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	3U9R	2.31	48.81	-3	110352	110021	5807	99.32	0.19044	0.18925	0.18	0.21325	0.2	RANDOM	27.757

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]
2.54			-1.67		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.836
r_dihedral_angle_3_deg	14.32
r_dihedral_angle_4_deg	14.269
r_dihedral_angle_1_deg	5.333
r_long_range_B_refined	2.799
r_long_range_B_other	2.799
r_scangle_other	1.416
r_mcangle_it	1.334
r_mcangle_other	1.334
r_angle_refined_deg	1.015
r_scbond_it	0.806
r_scbond_other	0.806
r_mcbond_it	0.744
r_mcbond_other	0.744
r_angle_other_deg	0.719
r_chiral_restr	0.058
r_bond_refined_d	0.005
r_bond_other_d	0.005
r_gen_planes_refined	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11687
Nucleic Acid Atoms
Solvent Atoms	573
Heterogen Atoms	24

Software

Software
Software Name	Purpose
MxDC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling