6OAD | pdb_00006oad

2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B from Escherichia coli str. K-12 substr. MG1655.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IJ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	Protein: 6.0 mg/ml, 0.01M Tris pH 8.3; Screen: PEGs II (H8), 0.2M Calcium acetate, 0.1M HEPES pH 7.5, 10% (w/v) PEG 8000. Cryo: reservoir + 20% Ethylene glycol.

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.667	α = 90
b = 114.761	β = 92.02
c = 161.171	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 300 mm CCD	C(111)	2019-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.05	30	98.8	0.098	0.098	0.112	0.054	11.9	4.1		338775		-3	30.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09	96.4		0.791	0.791	0.905	0.437	0.761	1.9	4.1

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3IJ3	2.05	29.88	321648	16698	98.62	0.17398	0.17185	0.21473	RANDOM	37.118

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]
1.68		-2.3	0.94		-2.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.462
r_dihedral_angle_4_deg	10.639
r_dihedral_angle_3_deg	9.454
r_long_range_B_refined	6.735
r_long_range_B_other	6.735
r_dihedral_angle_1_deg	3.09
r_scangle_other	1.718
r_angle_refined_deg	1.473
r_scbond_it	1.471
r_scbond_other	1.471
r_mcangle_it	1.408
r_mcangle_other	1.408
r_mcbond_it	0.828
r_mcbond_other	0.827
r_angle_other_deg	0.416
r_chiral_restr	0.072
r_gen_planes_refined	0.055
r_gen_planes_other	0.05
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	38883
Nucleic Acid Atoms
Solvent Atoms	3385
Heterogen Atoms	323

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MoRDa	phasing