4OU3 | pdb_00004ou3

Crystal structure of porcine aminopeptidase N complexed with CNGRCG tumor-homing peptide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	277	2 uL protein + 2 uL well solution (18% v/v PEG3350, 200 mM lithium sulfate, 100 mM HEPES, pH 7.2), VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 260.323	α = 90
b = 62.879	β = 100.59
c = 82.023	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		CCD	NOIR-1		2013-01-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2		ALS	4.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.92	50	97.9	0.079	0.079	20.7	3.8		95642

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.96	97		0.615	0.615	1.7	3.9

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	PDB ENTRY 4FKE	1.95	50	88648	4699	97.85	0.14285	0.14038	0.14	0.18956	0.19	RANDOM	49.799

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]
-0.59		-0.35	0.35		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_bonded	43.043
r_dihedral_angle_2_deg	40.055
r_sphericity_free	22.47
r_dihedral_angle_4_deg	16.523
r_dihedral_angle_3_deg	14.424
r_long_range_B_refined	10.931
r_scbond_it	10.842
r_mcangle_it	6.611
r_dihedral_angle_1_deg	6.328
r_mcbond_it	5.551
r_rigid_bond_restr	3.225
r_angle_refined_deg	1.614
r_chiral_restr	0.098
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7281
Nucleic Acid Atoms
Solvent Atoms	906
Heterogen Atoms	303

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing