9QWV | pdb_00009qwv

Trypanosoma cruzi enoyl-CoA hydratase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MJ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	292	10% PEG 8K, 0.2M MgCl2, 0.1M Tris-HCl

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.527	α = 90
b = 132.527	β = 90
c = 83.156	γ = 120

Symmetry
Space Group	H 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	PIXEL	DECTRIS PILATUS 2M		2022-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97628	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	39.09	100	0.074	0.083	0.036	1	13.1	10.6		36786			45.31

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	100		2.96	3.306	1.51	0.4	0.5	10.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	39.09	36784	1810	99.9	0.23	0.2182	0.2187	0.2529	0.2553	82.521

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]
2.7	1.35		2.7		-8.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.166
r_dihedral_angle_6_deg	14.103
r_lrange_it	6.696
r_lrange_other	6.687
r_dihedral_angle_2_deg	6.424
r_dihedral_angle_1_deg	6.388
r_scangle_it	4.276
r_scangle_other	4.249
r_mcangle_it	3.729
r_mcangle_other	3.728
r_scbond_it	2.758
r_scbond_other	2.673
r_mcbond_it	2.476
r_mcbond_other	2.476
r_angle_refined_deg	1.625
r_angle_other_deg	0.55
r_xyhbond_nbd_refined	0.259
r_nbd_refined	0.243
r_nbd_other	0.24
r_symmetry_xyhbond_nbd_refined	0.215
r_symmetry_nbd_other	0.209
r_symmetry_nbd_refined	0.202
r_nbtor_refined	0.178
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.08
r_xyhbond_nbd_other	0.076
r_symmetry_xyhbond_nbd_other	0.033
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3786
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing