4K5O | pdb_00004k5o

Phosphonic Arginine Mimetics as Inhibitors of the M1 Aminopeptidases from Plasmodium falciparum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EBH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	22% (v/v) PEG 8000, 10% (v/v) glycerol, 0.1 M Tris, 0.2 M MgCl2, vapor diffusion, hanging drop, temperature 298K, pH 8.5, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.056	α = 90
b = 109.35	β = 90
c = 118.518	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	CCD	ADSC QUANTUM 210r		2010-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.95467	Australian Synchrotron	MX1

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	1.9	80.37	96.4	0.144			1113693	75260

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	3EBH	1.9	64.01	74673	3801	95.61	0.1847	0.1816	0.18	0.2407	0.24	RANDOM	20.831

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]
0.11			-0.68		0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.547
r_dihedral_angle_4_deg	18.997
r_dihedral_angle_3_deg	14.533
r_dihedral_angle_1_deg	6.336
r_scangle_it	4.877
r_scbond_it	3.284
r_angle_refined_deg	1.89
r_mcangle_it	1.887
r_mcbond_it	1.148
r_chiral_restr	0.142

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.547
r_dihedral_angle_4_deg	18.997
r_dihedral_angle_3_deg	14.533
r_dihedral_angle_1_deg	6.336
r_scangle_it	4.877
r_scbond_it	3.284
r_angle_refined_deg	1.89
r_mcangle_it	1.887
r_mcbond_it	1.148
r_chiral_restr	0.142
r_bond_refined_d	0.024
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7200
Nucleic Acid Atoms
Solvent Atoms	1014
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
SCALA	data scaling
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 R01GM157729.