9E83 | pdb_00009e83

TMPRSS2 crystal structure following acylation by UCSF_157

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8V04

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
2.53	51.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.853	α = 90
b = 51.392	β = 91.01
c = 64.625	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 EIGER X 16M		2022-06-11	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	2.06	40	96.3	0.233	0.259	0.11	0.93	4.1	5.1		23755

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	2.06	2.1	86.1		0.942	1.061	0.476	0.548		4.1

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	2.07	39.29	22613	1128	96.21	0.20294	0.20004	0.2087	0.25991	0.265	RANDOM	35.376

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]
4.65		1.27	-2.81		-1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.239
r_long_range_B_refined	8.208
r_long_range_B_other	8.207
r_dihedral_angle_1_deg	7.76
r_dihedral_angle_2_deg	5.995
r_scangle_other	5.975
r_mcangle_other	5.067
r_mcangle_it	5.06
r_scbond_other	4.055
r_scbond_it	4.054
r_mcbond_it	3.51
r_mcbond_other	3.454
r_angle_refined_deg	1.501
r_angle_other_deg	0.539
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	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	2436
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	37

Software

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