5NTH | pdb_00005nth

Structure of Leucyl aminopeptidase from Leishmania major in complex with actinonin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NSK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.8 M Succinic acid pH 7.0, 3 % (w/v) 1,5-Diamino-pentane di-hydrochloride, 5 mM MnSO4, 5 mM actinonin

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.439	α = 90
b = 116.439	β = 90
c = 91.491	γ = 120

Symmetry
Space Group	P 3 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	PIXEL	DECTRIS PILATUS 6M		2013-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.97781	Diamond	I24

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	2.5	38.11	87.8	0.15	8.2	5.7		21850

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	2.5	2.6	90.2		0.747	2	5.6

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	MOLECULAR REPLACEMENT	THROUGHOUT	5NSK	2.5	38.11	20818	1031	86.72	0.19649	0.19397	0.2	0.24486	0.25	RANDOM	32.765

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]
-1.71	-0.85		-1.71		5.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.313
r_dihedral_angle_4_deg	17.932
r_dihedral_angle_3_deg	16.235
r_dihedral_angle_1_deg	6.993
r_long_range_B_refined	4.187
r_long_range_B_other	4.187
r_scangle_other	2.614
r_mcangle_it	2.474
r_mcangle_other	2.473
r_scbond_it	1.726
r_scbond_other	1.726
r_angle_refined_deg	1.642
r_mcbond_it	1.459
r_mcbond_other	1.456
r_angle_other_deg	1
r_chiral_restr	0.083
r_bond_refined_d	0.013
r_bond_other_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3893
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing