3QS1 | pdb_00003qs1

Crystal structure of KNI-10006 complex of Plasmepsin I (PMI) from Plasmodium falciparum

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	25 % PEG 2000 MME, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.69	α = 90
b = 93.69	β = 90
c = 160.12	γ = 90

Symmetry
Space Group	P 43

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 300 mm plate		2009-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

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	3.1	40	99	0.144	11.8	5.8	25066	24816

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	3.1	3.2	98.5		0.1636	1.2	5.8	2227

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.1	30	23562	1240	100	0.21544	0.21104	0.21	0.29965	0.3	RANDOM	49.496

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]
0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.653
r_dihedral_angle_3_deg	25.029
r_dihedral_angle_4_deg	11.753
r_dihedral_angle_1_deg	9.803
r_scangle_it	2.483
r_angle_refined_deg	2.161
r_scbond_it	1.486
r_mcangle_it	0.969
r_mcbond_it	0.484
r_chiral_restr	0.145

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.653
r_dihedral_angle_3_deg	25.029
r_dihedral_angle_4_deg	11.753
r_dihedral_angle_1_deg	9.803
r_scangle_it	2.483
r_angle_refined_deg	2.161
r_scbond_it	1.486
r_mcangle_it	0.969
r_mcbond_it	0.484
r_chiral_restr	0.145
r_bond_refined_d	0.021
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10406
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	240

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
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 R01GM157729.