5BRB | pdb_00005brb

Crystal structure of Q64E 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		296	28% PEG 1450, 100mM HEPES, 10mM calcium chloride, 0.5mM DTT, 0.5mM sodium azide

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.02	α = 90
b = 75.35	β = 97.72
c = 74.13	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		2013-09-07	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	2.526	75.35	97.2	0.156	0.187	0.101	5.6	3.2	14204	14204			40

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	2.51	2.65	81.4		0.441	0.441	0.298	2.3	3	1734

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	1O5X	2.53	73.57	13474	714	98.5	0.232	0.2288	0.23	0.2927	0.29	RANDOM	23.718

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]
-0.92		-0.63	-0.34		1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.058
r_dihedral_angle_4_deg	13.232
r_dihedral_angle_3_deg	12.491
r_dihedral_angle_1_deg	5.8
r_angle_refined_deg	1.07
r_angle_other_deg	0.87
r_mcangle_it	0.714
r_mcbond_it	0.407
r_mcbond_other	0.406
r_chiral_restr	0.057

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.058
r_dihedral_angle_4_deg	13.232
r_dihedral_angle_3_deg	12.491
r_dihedral_angle_1_deg	5.8
r_angle_refined_deg	1.07
r_angle_other_deg	0.87
r_mcangle_it	0.714
r_mcbond_it	0.407
r_mcbond_other	0.406
r_chiral_restr	0.057
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3667
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	2

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.