3DWE | pdb_00003dwe

Proteinase K by Classical hanging drop method after high X-Ray dose on ESRF ID14-2 beamline

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	20mg/ml of protein in 25mM HEPES pH7.0, reservoir solution composed by 25mM HEPES and 400mM Na/K tartrate at pH7.0. Onto the siliconized glass cover slides were mixed 4 microlitres of protein solution with 4 microlitres of reservoir solution., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.948	α = 90
b = 67.948	β = 90
c = 102.388	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	110	CCD	ADSC QUANTUM 4	Toroidal mirror	2007-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	1.2	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	0.99	56.615	86.1	0.09	0.09	5.6	5.8		114171

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	0.99	1.05	35		0.768	0.768	0.9	1.5	6600

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1PTK	0.99	48.06	113883	5724	86.12	0.221	0.221	0.22	0.222	0.22	RANDOM	7.099

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]
-0.03			-0.03		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.577
r_dihedral_angle_4_deg	13.98
r_dihedral_angle_3_deg	13.874
r_dihedral_angle_1_deg	5.501
r_scangle_it	1.399
r_angle_refined_deg	1.087
r_mcangle_it	1.049
r_scbond_it	1.034
r_mcbond_it	0.607
r_nbtor_refined	0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.577
r_dihedral_angle_4_deg	13.98
r_dihedral_angle_3_deg	13.874
r_dihedral_angle_1_deg	5.501
r_scangle_it	1.399
r_angle_refined_deg	1.087
r_mcangle_it	1.049
r_scbond_it	1.034
r_mcbond_it	0.607
r_nbtor_refined	0.314
r_symmetry_vdw_refined	0.308
r_symmetry_hbond_refined	0.252
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.127
r_metal_ion_refined	0.106
r_chiral_restr	0.076
r_bond_refined_d	0.005
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2021
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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.