3PTL | pdb_00003ptl

Crystal structure of proteinase K inhibited by a lactoferrin nonapeptide, Lys-Gly-Glu-Ala-Asp-Ala-Leu-Ser-Leu-Asp at 1.3 A resolution.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BJR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	tris HCl, CaCl2, NaNO3, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.054	α = 90
b = 68.054	β = 90
c = 106.75	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	77	CCD	MARRESEARCH	Mirror	2010-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	1.3	57.38	98.2	0.091	70		19396	19396			15.55

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	1.3	1.32	98.2		0.511	4

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 (All)	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	1BJR	1.3	57.38	19396	19396	1067	32.93	0.20225	0.2022	0.19964	0.2	0.24991	0.25	RANDOM	14.644

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]
-0.74			-0.74		1.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.222
r_dihedral_angle_4_deg	14.314
r_dihedral_angle_3_deg	13.468
r_dihedral_angle_1_deg	3.549
r_scangle_it	2.545
r_scbond_it	1.904
r_angle_refined_deg	1.537
r_mcangle_it	1.344
r_mcbond_it	0.854
r_chiral_restr	0.129

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.222
r_dihedral_angle_4_deg	14.314
r_dihedral_angle_3_deg	13.468
r_dihedral_angle_1_deg	3.549
r_scangle_it	2.545
r_scbond_it	1.904
r_angle_refined_deg	1.537
r_mcangle_it	1.344
r_mcbond_it	0.854
r_chiral_restr	0.129
r_bond_refined_d	0.017
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2101
Nucleic Acid Atoms
Solvent Atoms	438
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.