2HPO | pdb_00002hpo

Structure of Aminopeptidase N from E. coli Suggests a Compartmentalized, Gated Active Site

X-RAY DIFFRACTION

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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
3.52	65.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.438	α = 90
b = 120.438	β = 90
c = 170.561	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		2005-11-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9797, 0.9798, 0.9612	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.65	20	95.5	0.52	14.1		164250	164250

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	89.2		0.5	2	2.8	7598

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.65	19.94	164250	141768	4334	85.21	0.1785	0.15781	0.1571	0.16	0.18062	0.18	RANDOM	16.04

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]
-0.07	-0.03		-0.07		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.942
r_dihedral_angle_4_deg	17.604
r_dihedral_angle_3_deg	12.532
r_dihedral_angle_1_deg	5.483
r_sphericity_free	3.579
r_scangle_it	3.025
r_sphericity_bonded	2.574
r_scbond_it	1.927
r_mcangle_it	1.201
r_angle_refined_deg	1.171
r_rigid_bond_restr	1.098
r_mcbond_it	0.779
r_nbtor_refined	0.302
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.182
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.082
r_metal_ion_refined	0.037
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6940
Nucleic Acid Atoms
Solvent Atoms	1162
Heterogen Atoms	13

Software

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