2HPZ

Crystal structure of proteinase K complex with a synthetic peptide KLKLLVVIRLK at 1.69 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	50mM TRIS, 10mM CaCl2, 1M NaNO3, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.312	α = 90
b = 68.312	β = 90
c = 108.381	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	298	IMAGE PLATE	MARRESEARCH	MIRROR	2006-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5414

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.69	20	99.6	0.068	9.5		29433	29433			18.821

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.69	1.75	100		0.318	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1P7V	1.69	20	28397	28397	943	99.69	0.15983	0.1592	0.17944	RANDOM	20.99

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]
-0.15			-0.15		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.932
r_dihedral_angle_4_deg	21.338
r_dihedral_angle_3_deg	14.117
r_dihedral_angle_1_deg	5.801
r_scangle_it	3.529
r_scbond_it	2.363
r_angle_refined_deg	1.244
r_mcangle_it	1.23
r_mcbond_it	0.761
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.932
r_dihedral_angle_4_deg	21.338
r_dihedral_angle_3_deg	14.117
r_dihedral_angle_1_deg	5.801
r_scangle_it	3.529
r_scbond_it	2.363
r_angle_refined_deg	1.244
r_mcangle_it	1.23
r_mcbond_it	0.761
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.215
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.086
r_symmetry_hbond_refined	0.065
r_metal_ion_refined	0.038
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2230
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.