3S6B | pdb_00003s6b

Crystal structure of methionine aminopeptidase 1b from Plasmodium Falciparum, PF10_0150

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B3H	PDB entry 2b3h

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	27% PEG3350, 0.2 M Ammonium Acetate, 0.1 M Tris, 2 mM TCEP, 20 % glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.868	α = 90
b = 52.581	β = 116.67
c = 63.506	γ = 90

Symmetry
Space Group	P 1 21 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++		2011-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	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	1.9	40	98.1	0.069	11.7	3.5	27575	27052			25.7

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	1.9	1.93	78.8		0.637	1.81	2.3	1084

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB entry 2b3h	1.95	35	25494	25316	1297	99.3	0.1803	0.1779	0.18	0.2271	0.23	RANDOM	29.862

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]
-1.07		-3.1	-0.8		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.926
r_dihedral_angle_4_deg	16.617
r_dihedral_angle_3_deg	14.372
r_dihedral_angle_1_deg	5.642
r_scangle_it	3.103
r_scbond_it	2.007
r_angle_refined_deg	1.413
r_mcangle_it	1.077
r_mcbond_it	0.612
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.926
r_dihedral_angle_4_deg	16.617
r_dihedral_angle_3_deg	14.372
r_dihedral_angle_1_deg	5.642
r_scangle_it	3.103
r_scbond_it	2.007
r_angle_refined_deg	1.413
r_mcangle_it	1.077
r_mcbond_it	0.612
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2779
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	13

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
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.