7Y1X

Crystal structure of prolyl oligopeptidase from Microbulbifer arenaceous complex with PEG400 and MES

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	0.04 M MES monohydrate pH 6.0, 8.8% (v/v) polyethylene glycol 400

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.044	α = 90
b = 65.065	β = 104.948
c = 91.331	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	PIXEL	DECTRIS PILATUS3 S 2M		2021-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17B1	0.97944	SSRF	BL17B1

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	1.67	50	94.38	0.998	15.11	6.7		75931

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	1.67	1.7			0.899

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	THROUGHOUT	3MUN	1.67	31.651	75792	3688	94.38	0.161	0.1598	0.1887	16.037

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]
0.035		0.021	-0.128		0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.162
r_dihedral_angle_4_deg	17.816
r_dihedral_angle_3_deg	13.35
r_dihedral_angle_1_deg	7.298
r_lrange_it	5.041
r_scangle_it	3.876
r_scbond_it	2.637
r_angle_refined_deg	2.222
r_mcangle_it	2.157
r_mcbond_it	1.447

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.162
r_dihedral_angle_4_deg	17.816
r_dihedral_angle_3_deg	13.35
r_dihedral_angle_1_deg	7.298
r_lrange_it	5.041
r_scangle_it	3.876
r_scbond_it	2.637
r_angle_refined_deg	2.222
r_mcangle_it	2.157
r_mcbond_it	1.447
r_nbtor_refined	0.351
r_nbd_refined	0.229
r_symmetry_nbd_refined	0.22
r_symmetry_xyhbond_nbd_refined	0.179
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.13
r_gen_planes_refined	0.013
r_bond_refined_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5414
Nucleic Acid Atoms
Solvent Atoms	520
Heterogen Atoms	128

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	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 R01GM157729.