1WL9 | pdb_00001wl9

Structure of aminopeptidase P from E. coli

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AZ9	Published hexagonal structure without Mn or solvent atoms

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.3	277	Tris, PEG 4k, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.4	71.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.42	α = 90
b = 177.42	β = 90
c = 96.42	γ = 120

Symmetry
Space Group	P 64 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	IMAGE PLATE	RIGAKU RAXIS IIC	YALE MIRRORS	1997-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	1.9		93	24.4			65584		-3

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	1.9	1.97	63.4		5.69

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 (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	FOURIER SYNTHESIS	THROUGHOUT	Published hexagonal structure without Mn or solvent atoms	1.9	38.35	63537	1991	93.06	0.15243	0.15243	0.15185	0.16	0.17047	0.18	RANDOM	17.996

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]
0.25	0.12		0.25		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.877
r_dihedral_angle_4_deg	15.035
r_dihedral_angle_3_deg	11.876
r_dihedral_angle_1_deg	6.042
r_scangle_it	4.006
r_mcangle_it	2.815
r_scbond_it	2.635
r_mcbond_it	2.481
r_angle_refined_deg	1.28
r_angle_other_deg	0.829
r_mcbond_other	0.595
r_symmetry_vdw_other	0.286
r_symmetry_hbond_refined	0.211
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.205
r_nbd_other	0.182
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.151
r_nbtor_other	0.082
r_chiral_restr	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3500
Nucleic Acid Atoms
Solvent Atoms	607
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling