Experiment: 7QYH

Structure of plasmepsin II in complex with 2-aminoquinazolin-4(3H)-one based open-flap inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Z22

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298	0.1M citric acid, pH 4.5, 0.3M ammonium acetate, 25% PEG 4000, protein 10 mg/mL, vapour diffusion, sitting drop, time 4-8 weeks

Crystal Properties
Matthews coefficient	Solvent content
4.5	72.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.821	α = 90
b = 274.066	β = 90
c = 273.967	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-F		2021-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	3.33	137.03	86.8	0.987	4.6	13.1		15336			68.32

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.33	4.03			0.592

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	4Z22	3.33	137.03	1.35	15328	834	38.6	0.3117	0.3104	0.3091	0.3358	0.3366	80.9

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	11.0081
f_angle_d	1.6242
f_chiral_restr	0.1127
f_bond_d	0.0136
f_plane_restr	0.0065

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10420
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	29

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data processing