3QMJ | pdb_00003qmj

Crystal structure of Enoyl-CoA hydratase EchA8_6 from Mycobacterium marinum

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.7	290	Internal tracking number 218458A5. JCSG screen condition A5: 20% PEG3350, 0.2 M Magnesium formate. MymaA.00358.c.A1 PS00818 at 69.82 mg/ml., pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.906

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.82	α = 90
b = 115.82	β = 90
c = 115.82	γ = 90

Symmetry
Space Group	I 21 3

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	RIGAKU SATURN 944+		2011-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT

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	2.2	33.43	99.5	0.074	23.62	7.8	13294	13222		-3	37.348

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	2.2	2.26	96.7		0.461	5.8	7.1	972

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	MR	THROUGHOUT	PDB ENTRY 3FDU	2.2	33.43	13166	650	99.23	0.185	0.183	0.2	0.217	0.23	RANDOM	31.051

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.505
r_dihedral_angle_4_deg	20.292
r_dihedral_angle_3_deg	11.396
r_dihedral_angle_1_deg	6.058
r_scangle_it	3.324
r_scbond_it	2.022
r_angle_refined_deg	1.328
r_mcangle_it	1.295
r_angle_other_deg	0.955
r_mcbond_it	0.69
r_mcbond_other	0.14
r_chiral_restr	0.078
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1542
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	6

Software

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