3PVF | pdb_00003pvf

Structure of C126S mutant of Plasmodium falciparum triosephosphate isomerase complexed with PGA

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	20% PEG, HEPES buffer(pH 7.5), 10mM Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.51	α = 90
b = 63.1	β = 117.23
c = 53.2	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	IMAGE PLATE	MAR scanner 345 mm plate	mirror	2009-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.541

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	1.73	38.91	93.94	0.031	17.37	4.13		25341

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	1.732	1.777	83.2		0.125

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	MOLECULAR REPLACEMENT	THROUGHOUT	1LYX	1.73	26.25	24058	1283	94.38	0.15416	0.15193	0.16	0.19416	0.19	RANDOM	10.673

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	41.198
r_dihedral_angle_4_deg	12.729
r_dihedral_angle_3_deg	12.212
r_dihedral_angle_1_deg	6.301
r_scangle_it	5.286
r_scbond_it	3.386
r_angle_refined_deg	2.06
r_mcangle_it	1.997
r_mcbond_it	1.232
r_chiral_restr	0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.198
r_dihedral_angle_4_deg	12.729
r_dihedral_angle_3_deg	12.212
r_dihedral_angle_1_deg	6.301
r_scangle_it	5.286
r_scbond_it	3.386
r_angle_refined_deg	2.06
r_mcangle_it	1.997
r_mcbond_it	1.232
r_chiral_restr	0.16
r_bond_refined_d	0.026
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1955
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	9

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.