3DE1 | pdb_00003de1

Proteinase K by LB nanotemplate method after the third step of high X-Ray dose on ESRF ID23-1 beamline

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DE0	PDB ENTRY 3DE0

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 microL of protein solution with 4 microL of reservoir solution., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.669	α = 90
b = 67.669	β = 90
c = 101.625	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	CCD	ADSC QUANTUM 315		2007-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97625	ESRF	ID23-1

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	2	56.344	90.4	0.128	0.128	4.6	5.1		14864

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)
	2	2.11	90.7		0.258	0.258	2.1	5.2	2130

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 3DE0	2	34.84	14826	734	89.48	0.182	0.181	0.18	0.206	0.21	RANDOM	5.64

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]
-0.18			-0.18		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.371
r_dihedral_angle_4_deg	21.391
r_dihedral_angle_3_deg	15.11
r_dihedral_angle_1_deg	6.036
r_scangle_it	1.978
r_mcangle_it	1.56
r_scbond_it	1.465
r_angle_refined_deg	1.38
r_metal_ion_refined	1.379
r_mcbond_it	1.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.371
r_dihedral_angle_4_deg	21.391
r_dihedral_angle_3_deg	15.11
r_dihedral_angle_1_deg	6.036
r_scangle_it	1.978
r_mcangle_it	1.56
r_scbond_it	1.465
r_angle_refined_deg	1.38
r_metal_ion_refined	1.379
r_mcbond_it	1.008
r_symmetry_hbond_refined	0.513
r_symmetry_vdw_refined	0.443
r_nbtor_refined	0.316
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.216
r_chiral_restr	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

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
ADSC	data collection

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.