4K1F

Crystal structure of reduced tryparedoxin peroxidase from leishmania major at 2.34 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	20% PEG 3350, 0.2M NaSO4, 0.1M TRIS-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.811	α = 90
b = 226.203	β = 90
c = 91.719	γ = 90

Symmetry
Space Group	C 2 2 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		2013-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1	ELETTRA	5.2R

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	2.34	113.1	98.9	0.162	10.26		49646	49113		-3	41.222

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.34	2.48	94.7		1.07	1.189	1.65

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	PDB ENTRY 3TUE	2.34	113.1	49112	2489	98.91	0.1963	0.1936	0.2467	RANDOM	27.4724

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]
0.05			0.52		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.493
r_dihedral_angle_3_deg	16.816
r_dihedral_angle_4_deg	13.675
r_dihedral_angle_1_deg	6.356
r_scangle_it	3.301
r_scbond_it	2.009
r_angle_refined_deg	1.53
r_mcangle_it	1.229
r_mcbond_it	0.653
r_chiral_restr	0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.493
r_dihedral_angle_3_deg	16.816
r_dihedral_angle_4_deg	13.675
r_dihedral_angle_1_deg	6.356
r_scangle_it	3.301
r_scbond_it	2.009
r_angle_refined_deg	1.53
r_mcangle_it	1.229
r_mcbond_it	0.653
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7711
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	67

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	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 R01GM133198.