8V04 | pdb_00008v04

High resolution TMPRSS2 structure following acylation by nafamostat

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6KD5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	291	3 uL hanging drop (2:1 protein:precipitant) grown over precipitant solution containing 25%PEG4000, 0.2M ammonium sulfate, and 0.1M sodium acetate pH 4.6. Protein (10 mg/mL) was in a buffer containing 25 mM Tris pH 8.0, 75 mM NaCl, and 2 mM CaCl2

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.757	α = 90
b = 50.502	β = 91.6
c = 64.578	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 EIGER2 X 16M		2022-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97918	APS	24-ID-C

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	1.58	40	92.8	0.099	0.127	0.079	0.988	8.7	2.2		94364

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	1.58	1.61	91.6		0.663	0.851	0.528	0.625		2.2

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	1.58	39.81	49216	2463	99	0.15695	0.15571	0.17	0.18084	0.19	RANDOM	19.803

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]
2.51		0.88	-0.25		-2.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.824
r_dihedral_angle_2_deg	7.446
r_long_range_B_refined	6.889
r_long_range_B_other	6.887
r_dihedral_angle_1_deg	6.732
r_scangle_other	4.64
r_mcangle_other	3.125
r_mcangle_it	3.123
r_scbond_it	3.113
r_scbond_other	3.112
r_mcbond_it	2.079
r_mcbond_other	2.077
r_angle_refined_deg	1.659
r_angle_other_deg	0.596
r_chiral_restr	0.085
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2614
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	128

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing