5BMW

Crystal structure of T75V mutant of Triosephosphate isomerase from Plasmodium falciparum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O5X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	296	20% PEG 1450, 100 mM MES buffer, 10 mM Calcium chloride, 0.5 mM EDTA, 0.5 mM DTT, 0.5 mM sodium azide

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.21	α = 90
b = 76.02	β = 97.47
c = 74.36	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	IMAGE PLATE	MAR scanner 345 mm plate		2014-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.541

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.859	73.73	99.8	0.056	0.061	0.025	22.2	5.6	36392	36392

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.96	98.4		0.156	0.156	0.075	4.7	5.2	5211

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	1O5X	1.86	73.73	34547	1816	99.74	0.134	0.1314	0.1824	RANDOM	11.586

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]
0.22		-0.02	-0.16		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.944
r_dihedral_angle_3_deg	11.758
r_dihedral_angle_4_deg	11.258
r_dihedral_angle_1_deg	6.47
r_angle_refined_deg	1.802
r_mcangle_it	1.303
r_angle_other_deg	1.033
r_mcbond_it	0.896
r_mcbond_other	0.89
r_chiral_restr	0.111

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.944
r_dihedral_angle_3_deg	11.758
r_dihedral_angle_4_deg	11.258
r_dihedral_angle_1_deg	6.47
r_angle_refined_deg	1.802
r_mcangle_it	1.303
r_angle_other_deg	1.033
r_mcbond_it	0.896
r_mcbond_other	0.89
r_chiral_restr	0.111
r_bond_refined_d	0.019
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	3859
Nucleic Acid Atoms
Solvent Atoms	483
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	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 R01GM157729.