5NTD | pdb_00005ntd

Structure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Bestatin

X-RAY DIFFRACTION

---

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	0.1 M HEPES pH 7.0, 40 % (v/v) MPD, 5 mM MnCl2, 5 mM bestatin

Crystal Properties
Matthews coefficient	Solvent content
2.51	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.26	α = 90
b = 143.45	β = 95.54
c = 268.03	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	PIXEL	DECTRIS PILATUS 6M		2013-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	2.3	80.33	99.7	0.091	9.1	3.9		290030

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	2.3	2.34			0.523	2.1	3.7	14130

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	2.3	80.33	275670	14322	99.71	0.18995	0.18871	0.2	0.21375	0.22	RANDOM	33.041

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]
2.59		-1.71	-0.65		-1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.752
r_dihedral_angle_4_deg	14.75
r_dihedral_angle_3_deg	13.499
r_dihedral_angle_1_deg	5.888
r_long_range_B_refined	4.971
r_long_range_B_other	4.971
r_scangle_other	3.284
r_mcangle_it	2.491
r_mcangle_other	2.491
r_angle_other_deg	2.348
r_scbond_it	2.161
r_scbond_other	2.14
r_mcbond_it	1.588
r_mcbond_other	1.588
r_angle_refined_deg	1.475
r_chiral_restr	0.079
r_bond_refined_d	0.015
r_bond_other_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.007
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	45572
Nucleic Acid Atoms
Solvent Atoms	2798
Heterogen Atoms	436

Software

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