7QE9 | pdb_00007qe9

Human cationic trypsin (TRY1) complexed with serine protease inhibitor Kazal type 1 N34S (SPINK1 N34S)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CGI	1TRN_A, 1CGI_I
experimental model	PDB	1TRN	1TRN_A, 1CGI_I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	1 uL protein solution (20 mg/mL in 20 mM Hepes pH 7.4, 150 mM NaCl) + 1 uL well solution (15% PEG 4000, 0.3 M AS), cryo: 15% PEG 4000, 0.3 M AS, 8% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.555	α = 90
b = 76.555	β = 90
c = 189.719	γ = 120

Symmetry
Space Group	P 31 2 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 PILATUS3 S 2M	DCM Si(111)	2020-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.1	50	99.8	0.174	0.179	0.999	14.8	19.7		38593		-3	50.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.22	98.7		3.172	3.256	0.411	1	19.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1TRN_A, 1CGI_I	2.1	50	38518	1899	99.974	0.195	0.1927	0.2	0.2336	0.23	50.032

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]
0.174	0.087		0.174		-0.565

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.453
r_dihedral_angle_4_deg	21.506
r_dihedral_angle_3_deg	17.006
r_dihedral_angle_1_deg	7.786
r_lrange_it	6.422
r_lrange_other	6.402
r_scangle_it	3.804
r_scangle_other	3.759
r_mcangle_it	2.727
r_mcangle_other	2.727
r_scbond_it	2.548
r_scbond_other	2.52
r_mcbond_it	1.889
r_mcbond_other	1.889
r_angle_refined_deg	1.838
r_angle_other_deg	1.354
r_symmetry_nbd_refined	0.266
r_nbd_other	0.226
r_symmetry_xyhbond_nbd_refined	0.226
r_nbd_refined	0.194
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.165
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.078
r_bond_refined_d	0.013
r_symmetry_xyhbond_nbd_other	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4241
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing