3QXZ | pdb_00003qxz

Crystal structure of a probable enoyl-CoA hydratase/isomerase from Mycobacterium abscessus

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	MyabA.00358.c.A1 PS00900 at 53.9 mg/mL 3C cleaved against PACT screen condition H10, 0.2 M NaKHPO4, 0.1 M BisTris propane pH 6.5, 25% PEG3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 219606h10, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.17	α = 90
b = 76.17	β = 90
c = 122.52	γ = 120

Symmetry
Space Group	P 32

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	ADSC QUANTUM 315r		2011-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1		ALS	5.0.1

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	1.35	50	99.9	0.055	15.11	4.5	174722	174539		-3	18.15

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	1.35	1.39	99.8		0.49	2.9	4.1	13000

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	PDB ENTRY 3GOW	1.35	50	174539	8736	99.89	0.1522	0.1514	0.16	0.1689	0.17	RANDOM	13.9098

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]
0.04	0.02		0.04		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.841
r_dihedral_angle_4_deg	17.536
r_dihedral_angle_3_deg	11.169
r_dihedral_angle_1_deg	5.453
r_scangle_it	3.246
r_scbond_it	1.994
r_angle_refined_deg	1.372
r_mcangle_it	1.239
r_mcbond_it	0.707
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.841
r_dihedral_angle_4_deg	17.536
r_dihedral_angle_3_deg	11.169
r_dihedral_angle_1_deg	5.453
r_scangle_it	3.246
r_scbond_it	1.994
r_angle_refined_deg	1.372
r_mcangle_it	1.239
r_mcbond_it	0.707
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5592
Nucleic Acid Atoms
Solvent Atoms	809
Heterogen Atoms	70

Software

Software
Software Name	Purpose
MOSFLM	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
XDS	data reduction

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.