9JQ9 | pdb_00009jq9

Crystal structure of Plasmoredoxin from Plasmodium falciparum a disulfide oxidoreductase protein unique to Plasmodium species

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	ModelArchive		MR done using Mrbump in ccp4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	ammonium acetate, ammonium sulphate, PEG-8000

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.551	α = 90
b = 50.499	β = 90
c = 78.571	γ = 90

Symmetry
Space Group	P 21 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 PILATUS3 R 1M		2021-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	Excillum MetalJet D2+ 160 kV	1.36

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	1.9	41.3	99.43	0.06169	0.0644	0.01791	0.999	26.25	11.6		15673			22.05

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	1.9	1.97	98.25		0.4582	0.4582	0.1798	0.957	3.77	6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	41.3	1.35	15667	777	99.45	0.2058	0.2041	0.2003	0.2367	0.2351	24.35

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
f_dihedral_angle_d	6.0825
f_angle_d	0.9351
f_chiral_restr	0.0575
f_plane_restr	0.0094
f_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1429
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHENIX	phasing
MrBUMP	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.