3B2P | pdb_00003b2p

Crystal structure of E. coli Aminopeptidase N in complex with arginine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HPO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	1.8 M Sodium malonate pH=7/0, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.204	α = 90
b = 120.204	β = 90
c = 169.655	γ = 120

Symmetry
Space Group	P 31 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	KOHZU: Double Crystal Si(111)	2007-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0000	ALS	8.2.2

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	2	50	99.9	0.1	0.08	13.2	5.6	95605	95605	2	2	22.885

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	2	2.07	99.4		0.57	0.5	2.4	5	9360

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2HPO	2	44.37	20	2	95736	92657	2855	99.77	0.15448	0.15343	0.16	0.18846	0.19	RANDOM	20.646

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
r_dihedral_angle_2_deg	36.97
r_dihedral_angle_4_deg	18.644
r_dihedral_angle_3_deg	14.035
r_dihedral_angle_1_deg	6.017
r_scangle_it	4.185
r_scbond_it	2.53
r_angle_refined_deg	1.434
r_mcangle_it	1.393
r_mcbond_it	0.731
r_nbtor_refined	0.297
r_symmetry_vdw_refined	0.239
r_symmetry_hbond_refined	0.236
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.184
r_metal_ion_refined	0.141
r_chiral_restr	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6940
Nucleic Acid Atoms
Solvent Atoms	765
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
APEX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing