Experiment: 4WWV

Aminopeptidase APDkam598 from the archaeon Desulfurococcus kamchatkensis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XFO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	7.5	293	The reservoir solution contained 0.1 M HEPES, pH 7.0, 0.8 M ammonium sulfate, and glycerol. The crystals were grown over a period of several months.

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 234.323	α = 90
b = 234.323	β = 90
c = 234.323	γ = 90

Symmetry
Space Group	F 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX-225		2013-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

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	3	50	99.9	0.079	19.4	5.1	21480	21317

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	3.05	100		2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MOLECULAR REPLACEMENT	FREE R-VALUE	1XFO	3.006	47.831	1.34	20238	1044	94.98	0.2074	0.2041	0.2079	0.2634	0.2647	36.05

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.832
f_angle_d	1.46
f_chiral_restr	0.068
f_bond_d	0.013
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5479
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
BALBES	phasing