6BV1

Crystal structure of porcine aminopeptidase-N with Aspartic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FKE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	277	18% PEG3350, 200 MM LITHIUM SULFATE, 100 MM HEPES

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 259.81	α = 90
b = 62.682	β = 100.4
c = 81.717	γ = 90

Symmetry
Space Group	C 1 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	CCD	ADSC QUANTUM 315		2012-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	1	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	50	97.8	0.062	19.64	3.7		85779

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	97.2		0.574	2.55		8437

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4FKE	2	50	81490	4288	97.74	0.20973	0.20744	0.2527	RANDOM	32.152

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]
-0.43		0.77	0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.095
r_dihedral_angle_4_deg	18.689
r_dihedral_angle_3_deg	16.176
r_dihedral_angle_1_deg	7.333
r_rigid_bond_restr	6.026
r_sphericity_free	6.025
r_sphericity_bonded	3.142
r_angle_other_deg	1.96
r_long_range_B_refined	1.871
r_long_range_B_other	1.83
r_mcangle_it	1.758
r_mcangle_other	1.758
r_mcbond_it	1.628
r_mcbond_other	1.627
r_scbond_it	1.583
r_scangle_other	1.575
r_scbond_other	1.533
r_angle_refined_deg	1.132
r_chiral_restr	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.005
r_bond_other_d	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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7241
Nucleic Acid Atoms
Solvent Atoms	842
Heterogen Atoms	382

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing