7VGC | pdb_00007vgc

Crystal structure of prolyl oligopeptidase from Microbulbifer arenaceous complex with a transition state analog inhibitor ZPR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VGB

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.108	α = 90
b = 65.622	β = 105.29
c = 91.765	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	0.979	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	2.722	30.96	96.28	0.924	5.75	5.1		18620

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	2.722	2.82			0.924

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7VGB	2.722	30.96	18608	931	96.352	0.199	0.1952	0.2	0.2708	0.27	44.608

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]
-0.225		-0.984	-0.297		0.922

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.723
r_dihedral_angle_3_deg	18.201
r_dihedral_angle_4_deg	15.886
r_dihedral_angle_1_deg	7.923
r_lrange_it	6.893
r_mcangle_it	4.311
r_scangle_it	4.251
r_scbond_it	2.81
r_mcbond_it	2.693
r_angle_refined_deg	1.242

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.723
r_dihedral_angle_3_deg	18.201
r_dihedral_angle_4_deg	15.886
r_dihedral_angle_1_deg	7.923
r_lrange_it	6.893
r_mcangle_it	4.311
r_scangle_it	4.251
r_scbond_it	2.81
r_mcbond_it	2.693
r_angle_refined_deg	1.242
r_nbtor_refined	0.324
r_symmetry_xyhbond_nbd_refined	0.248
r_nbd_refined	0.239
r_symmetry_nbd_refined	0.234
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.101
r_gen_planes_refined	0.005
r_bond_refined_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5439
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	26

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.