6KUD

Crystal structure of Plasmodium falciparum histo-aspartic protease (HAP) zymogen (Form 3)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.2M Lithium citrate tribasic tetrahydrate, 20% w/v Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
3	58.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.19	α = 90
b = 69.91	β = 125.71
c = 73.26	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	RIGAKU RAXIS IV++		2015-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.9	29.19	97.4	0.11	12.15	3.8		11027

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	2.9	3			0.96	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.9	29.19	10474	552	98.07	0.1876	0.1843	0.2504	RANDOM	61.619

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]
-2.42		-0.57	2.46		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.558
r_dihedral_angle_3_deg	19.827
r_dihedral_angle_4_deg	11.551
r_dihedral_angle_1_deg	7.996
r_angle_refined_deg	1.719
r_angle_other_deg	1.053
r_chiral_restr	0.111
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.558
r_dihedral_angle_3_deg	19.827
r_dihedral_angle_4_deg	11.551
r_dihedral_angle_1_deg	7.996
r_angle_refined_deg	1.719
r_angle_other_deg	1.053
r_chiral_restr	0.111
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2988
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	12

Software

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