3B34 | pdb_00003b34

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

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	2M Sodium Malonate, pH=7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.53	65.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.582	α = 90
b = 120.582	β = 90
c = 170.761	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		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0	ALS	8.2.2

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	1.3	50	99.2	0.123	8.2	8.9		346171	2	2	14.6

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	1.3	1.32	89.9		0.49	0.49	1.18	1.9	15484

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2HPO	1.3	50	487111	339183	10333	97.16	0.177	0.177	0.18	0.19416	Random	18.757

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]
0.05	0.03		0.05		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.853
r_dihedral_angle_4_deg	17.004
r_dihedral_angle_3_deg	12.202
r_dihedral_angle_1_deg	5.557
r_sphericity_bonded	4.396
r_sphericity_free	3.732
r_scangle_it	3.342
r_scbond_it	3.078
r_rigid_bond_restr	3.061
r_mcangle_it	1.356
r_angle_refined_deg	1.15
r_mcbond_it	0.804
r_nbtor_refined	0.296
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.164
r_symmetry_hbond_refined	0.149
r_metal_ion_refined	0.14
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6940
Nucleic Acid Atoms
Solvent Atoms	1113
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing