2HPT | pdb_00002hpt

Crystal Structure of E. coli PepN (Aminopeptidase N)in complex with Bestatin

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	1.8 M Sodium Malonate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.54	65.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.67	α = 90
b = 120.67	β = 90
c = 170.84	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		2005-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.0000	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	50	100			64583	64583		2

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	2.3	2.38	100

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 (All)	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 2HPO	2.3	49.94	64583	61128	3258	99.99	0.181	0.15655	0.1541	0.1542	0.20231	0.2024	RANDOM	18.076

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]
0.2	0.1		0.2		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.258
r_dihedral_angle_4_deg	20.137
r_dihedral_angle_3_deg	15.698
r_dihedral_angle_1_deg	6.453
r_scangle_it	4.343
r_scbond_it	2.781
r_angle_refined_deg	1.649
r_mcangle_it	1.515
r_mcbond_it	0.941
r_symmetry_hbond_refined	0.351
r_nbtor_refined	0.299
r_xyhbond_nbd_refined	0.257
r_symmetry_vdw_refined	0.25
r_nbd_refined	0.213
r_metal_ion_refined	0.115
r_chiral_restr	0.105
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6940
Nucleic Acid Atoms
Solvent Atoms	739
Heterogen Atoms	41

Software

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