8B1Y | pdb_00008b1y

STRUCTURE OF PORCINE PANCREATIC ELASTASE BOUND TO A FRAGMENT OF A 5-AZAINDAZOLE INHIBITOR

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.1	296	SODIUM SULFATE, SODIUM ACETATE

Crystal Properties
Matthews coefficient	Solvent content
1.81	31.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.09	α = 90
b = 58.05	β = 90
c = 74.41	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 6M		2020-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.9999	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.12	30	99.2	0.069	0.072	0.999	17.84	10.816		83858			14.089

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.12	1.15	95.3		0.759	0.829	0.773	2.38	6.328

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	3HGP	1.12	30	79711	4139	99.22	0.1279	0.1268	0.14	0.1499	0.16	RANDOM	12.634

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]
0.09			-0.29		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.158
r_dihedral_angle_4_deg	19.327
r_dihedral_angle_3_deg	11.507
r_dihedral_angle_1_deg	6.705
r_rigid_bond_restr	5.495
r_angle_refined_deg	2.219
r_angle_other_deg	1.679
r_chiral_restr	0.145
r_bond_refined_d	0.023
r_gen_planes_refined	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.158
r_dihedral_angle_4_deg	19.327
r_dihedral_angle_3_deg	11.507
r_dihedral_angle_1_deg	6.705
r_rigid_bond_restr	5.495
r_angle_refined_deg	2.219
r_angle_other_deg	1.679
r_chiral_restr	0.145
r_bond_refined_d	0.023
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1813
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	17

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	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.