2XE4 | pdb_00002xe4

Structure of Oligopeptidase B from Leishmania major

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.2		PROTEIN WAS DIALYZED INTO 50 MM TRIS, PH 8.0 AND INCUBATED WITH 10 MM ANTIPAIN FOR 30 MINS. THIS WAS MIXED IN A 1:1 RATIO WITH 25% 1,2 PROPANEDIOL, 10% GLYCEROL, 5 % PEG300 AND 0.1 M PHOSPHATE CITRATE, PH 4.2

Crystal Properties
Matthews coefficient	Solvent content
4.2	71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.478	α = 90
b = 142.776	β = 90
c = 208.919	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103	IMAGE PLATE	MARRESEARCH	MIRRORS	2008-06-10	M	SINGLE WAVELENGTH
2	1	x-ray	103	CCD	MARRESEARCH			M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007
2	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	1.65	32	98.4	0.06	8.8	3.3		167772		1.5	29.5

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	1.65	1.71	100		0.46	1.7	3

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	SAD	THROUGHOUT	NONE	1.65	117.851	167169	8321	98.007	0.142	0.1403	0.1459	0.178	0.1822	RANDOM	41.338

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]
2.673			-1.71		-0.963

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.738
r_dihedral_angle_4_deg	15.532
r_dihedral_angle_3_deg	12.49
r_scangle_it	9.512
r_scbond_it	6.794
r_dihedral_angle_1_deg	6.661
r_mcangle_it	4.118
r_rigid_bond_restr	3.903
r_mcbond_it	2.833
r_angle_refined_deg	2.353
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.222
r_symmetry_hbond_refined	0.215
r_chiral_restr	0.209
r_xyhbond_nbd_refined	0.161
r_metal_ion_refined	0.065
r_bond_refined_d	0.035
r_gen_planes_refined	0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5809
Nucleic Acid Atoms
Solvent Atoms	721
Heterogen Atoms	326

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
SCALA	data scaling
autoSHARP	phasing
SHELXCD	phasing
SHELXD	phasing