9SI4 | pdb_00009si4

Structure of human neutrophil elastase in complex with a 5,8-dihydro[1,2,4]triazolo[4,3-a]pyrimidin-3(2H)-one inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q77

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	18% PEG-3350, 0.2M ammonium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.16	α = 90
b = 73.16	β = 90
c = 70.15	γ = 120

Symmetry
Space Group	P 63

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		2014-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.14	36.61	78.8	0.035	33.7	8.8		61016

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.14	1.17			0.329

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.14	36.61	57914	3094	78.65	0.13507	0.13402	0.1395	0.1549	0.1586	RANDOM	19.267

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]
0.25	0.12		0.25		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_other	20.985
r_scbond_other	20.399
r_scbond_it	19.979
r_long_range_B_refined	18.902
r_long_range_B_other	18.815
r_dihedral_angle_3_deg	12.952
r_mcangle_other	9.615
r_mcangle_it	9.577
r_dihedral_angle_1_deg	7.538
r_mcbond_it	7.179
r_mcbond_other	7.156
r_rigid_bond_restr	4.39
r_angle_refined_deg	1.403
r_angle_other_deg	0.504
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1636
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	115

Software

Software
Software Name	Purpose
PDB-REDO	refinement
PHASER	phasing
xia2	data scaling
Coot	model building
autoPROC	data reduction