8B53 | pdb_00008b53

Structure of porcine pancreatic elastase bound to a fragment of a 4-azaindole inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QNJ	1QNJ

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 = 50.019	α = 90
b = 57.91	β = 90
c = 74.519	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)	Rpim 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	1.25	22.25	100	0.103	0.108	0.032	0.997	11.3	11.3		60617

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.27	100		0.411	0.432	0.13	0.932		10.8

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	1QNJ	1.25	22.25	57536	3007	99.96	0.1135	0.1123	0.11	0.1354	0.14	RANDOM	11.145

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]
-0.29			0.19		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.307
r_dihedral_angle_4_deg	19.517
r_dihedral_angle_3_deg	10.654
r_dihedral_angle_1_deg	6.682
r_rigid_bond_restr	2.82
r_angle_refined_deg	1.972
r_angle_other_deg	1.622
r_chiral_restr	0.125
r_bond_refined_d	0.017
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1819
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms	21

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing