Experiment: 4E36

Crystal structure of the human Endoplasmic Reticulum Aminopeptidase 2 variant N392K

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SE6	PDB ENTRY 3SE6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	10% PEG 8000, 20% ethylene glycol, 20 mM glycine, 20 mM DL-lysine, 20 mM DL-serine, 20 mM DL-alanine, 20 mM sodium L-glutamate, 31 mM imidazole, 69 mM MES. Protein mixed 1:4 with LPL peptide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.34	α = 90
b = 134.45	β = 90.85
c = 127.37	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 2M		2011-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.22	59.45	99.1				71589		-5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.22	3.39	99.39

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	isomorphous replacement	PDB ENTRY 3SE6	3.22	10.996	1.12	77873	69634	3912	89.42	0.2113	0.2087	0.218	0.2608	0.2701

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]
5.1882		15.2206	-15.5805		6.3347

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	19.505
f_angle_d	1.12
f_chiral_restr	0.065
f_bond_d	0.007
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13985
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	236

Software

Software
Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling