6K8M

High resolution crystal structure of proteinase K with thiourea

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	273	1.28M ammonium sulfate, 0.1M Tris-HCl, pH 7.2

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.842	α = 90
b = 67.842	β = 90
c = 102.377	γ = 90

Symmetry
Space Group	P 43 21 2

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	Bruker PHOTON II		2019-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER IMUS MICROFOCUS	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.45	19.79	99.9	0.065	0.092	0.99	12.4	1.9		43099			14.42

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.45	99.5		0.557	0.787	1.9	1.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1PEK	1.45	19.79	40867	2162	99.9	0.1688	0.1682	0.1795	RANDOM	6.304

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]
0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.722
r_dihedral_angle_4_deg	14.647
r_dihedral_angle_3_deg	12.863
r_dihedral_angle_1_deg	6.718
r_angle_other_deg	2.479
r_angle_refined_deg	1.747
r_mcangle_it	0.885
r_mcbond_it	0.607
r_mcbond_other	0.57
r_chiral_restr	0.082
r_bond_other_d	0.038
r_gen_planes_other	0.017
r_bond_refined_d	0.012
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2025
Nucleic Acid Atoms
Solvent Atoms	226
Heterogen Atoms	18

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
Aimless	data scaling
Coot	model building