7Y1S

Crystal structure of apo leucyl aminopeptidase from Bacillus amyloliquefaciens

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	0.5 M succinic acid (pH 7.0), 0.1 M Bis-Tris propane (pH 7.0)

Crystal Properties
Matthews coefficient	Solvent content
4.78	74.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 200.245	α = 90
b = 200.245	β = 90
c = 89.022	γ = 120

Symmetry
Space Group	P 63 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	100	PIXEL	DECTRIS PILATUS3 S 2M		2019-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.9793	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.748	50	99.24	0.996	21.69	30.3		27747

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.748	2.848			0.97

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-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3JRU	2.748	37.871	27669	1332	99.133	0.172	0.17	0.2118	58.642

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]
-1.055	-0.527		-1.055		3.422

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.235
r_dihedral_angle_4_deg	24.148
r_dihedral_angle_3_deg	20.197
r_lrange_it	11.52
r_scangle_it	10.718
r_scbond_it	8.269
r_mcangle_it	7.512
r_dihedral_angle_1_deg	7.338
r_mcbond_it	5.573
r_angle_refined_deg	1.855

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.235
r_dihedral_angle_4_deg	24.148
r_dihedral_angle_3_deg	20.197
r_lrange_it	11.52
r_scangle_it	10.718
r_scbond_it	8.269
r_mcangle_it	7.512
r_dihedral_angle_1_deg	7.338
r_mcbond_it	5.573
r_angle_refined_deg	1.855
r_nbtor_refined	0.318
r_symmetry_nbd_refined	0.259
r_nbd_refined	0.242
r_symmetry_xyhbond_nbd_refined	0.227
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.139
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3714
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	7

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.