8J7C | pdb_00008j7c

Crystal structure of triosephosphate isomerase from Leishmania orientalis at 1.88A with an arsenic ion bound at Cys57

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	I2APN2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	5.9	291.15	Equal volumes (1.0 microliter) of enzyme (24.2 mg/ml in 50 mM potassium phosphate buffer, pH 8.0, containing 50 mM KCl, 5 mM DTT, and 10% glycerol) and precipitant (PEG8000 18% w/v in 0.2 mM calcium acetate hydrate, 0.1 M and sodium cacodylate trihydrate, pH 5.9)

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.44	α = 90
b = 76.45	β = 101.14
c = 94.94	γ = 90

Symmetry
Space Group	C 1 2 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	MAR CCD 165 mm	spherical mirror for CM and toroidal mirror for M	2015-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLRI BEAMLINE BL7.2W	1.5500	SLRI	BL7.2W

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	1.88	21.56	98.6	0.082	0.101	0.059	0.991	11.9	2.8		46160			6.92

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	1.88	1.92	81.2		0.549	0.682	0.399	0.598	2.4	2.6

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 (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	FREE R-VALUE	1.88	19.98	43811	2354	99.06	0.17366	0.17148	0.18	0.21377	0.22	RANDOM	16.047

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_3_deg	13.959
r_dihedral_angle_1_deg	7.052
r_dihedral_angle_2_deg	5.926
r_long_range_B_refined	4.584
r_long_range_B_other	4.322
r_scangle_other	2.966
r_scbond_it	1.897
r_scbond_other	1.897
r_mcangle_it	1.881
r_mcangle_other	1.881
r_angle_refined_deg	1.564
r_mcbond_it	1.321
r_mcbond_other	1.32
r_angle_other_deg	0.517
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3712
Nucleic Acid Atoms
Solvent Atoms	491
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
pointless	data scaling
MOSFLM	data reduction
PHASER	phasing