6UPF

Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	283	0.05 M Tris-HCl pH 7.5, 0.05 M NaCl, 1 mM EDTA, 15% PEG 4000 and 2 mM 2-PG

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.83	α = 90
b = 75.16	β = 90
c = 151.92	γ = 90

Symmetry
Space Group	P 2 21 21

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		2019-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.4586	LNLS	W01B-MX2

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	1.65	75.96	99	0.084	0.099	0.052	0.995	8.5	3.4		66128

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	1.65	1.68	99.4		0.714	0.845	0.442	0.523		3.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4poc	1.65	75.96	62725	3334	98.7	0.1646	0.1628	0.197	RANDOM	19.827

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]
-0.03			0.14		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.649
r_dihedral_angle_4_deg	15.113
r_dihedral_angle_3_deg	13.923
r_dihedral_angle_1_deg	6.252
r_angle_refined_deg	1.953
r_angle_other_deg	1.067
r_chiral_restr	0.125
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.649
r_dihedral_angle_4_deg	15.113
r_dihedral_angle_3_deg	13.923
r_dihedral_angle_1_deg	6.252
r_angle_refined_deg	1.953
r_angle_other_deg	1.067
r_chiral_restr	0.125
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3718
Nucleic Acid Atoms
Solvent Atoms	702
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

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 R01GM133198.