3QK8 | pdb_00003qk8

Crystal structure of enoyl-coA hydratase EchA15 from Mycobacterium marinum in complex with an unknown ligand

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WZ8	PDB ENTRY 1WZ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	290	Internal tracking number 218997A9. JCSG screen condition A9: 20% PEG3350, 0.2 M ammonium chloride. MymaA.00829.b.A1 PS00862 at 43.78mg/ml., pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.99	α = 90
b = 129.53	β = 108.57
c = 78.61	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315		2010-12-21	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	1.6	48.883	98.4	0.045	23.92	4.5256	184428	181397		-3	21.199

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	1.6	1.64	88.7		0.314	4	3.671	13629

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	MR	THROUGHOUT	PDB ENTRY 1WZ8	1.6	48.883	184428	181313	9122	98.39	0.138	0.138	0.137	0.15	0.164	0.18	RANDOM	14.753

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]
-0.01		0.15	0.36		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.665
r_dihedral_angle_4_deg	16.6
r_dihedral_angle_3_deg	11.828
r_dihedral_angle_1_deg	5.84
r_scangle_it	4.014
r_scbond_it	2.508
r_angle_refined_deg	1.633
r_mcangle_it	1.518
r_angle_other_deg	1.136
r_mcbond_it	0.906

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.665
r_dihedral_angle_4_deg	16.6
r_dihedral_angle_3_deg	11.828
r_dihedral_angle_1_deg	5.84
r_scangle_it	4.014
r_scbond_it	2.508
r_angle_refined_deg	1.633
r_mcangle_it	1.518
r_angle_other_deg	1.136
r_mcbond_it	0.906
r_mcbond_other	0.29
r_chiral_restr	0.104
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11683
Nucleic Acid Atoms
Solvent Atoms	1292
Heterogen Atoms	109

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	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.