6ZHJ

3D electron diffraction structure of thermolysin from Bacillus thermoproteolyticus

ELECTRON CRYSTALLOGRAPHY

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92	α = 90
b = 92	β = 90
c = 127.48	γ = 120

Symmetry
Space Group	P 61 2 2

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
ELECTRON CRYSTALLOGRAPHY	MOLECULAR REPLACEMENT	THROUGHOUT	1FJ3	3.26	37.52	4293	237	84.17	0.2142	0.2101	0.2923	RANDOM	29.4

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]
0.04	0.02		0.04		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.957
r_dihedral_angle_3_deg	18.072
r_dihedral_angle_4_deg	15.968
r_dihedral_angle_1_deg	8.426
r_angle_refined_deg	1.154
r_angle_other_deg	0.834
r_chiral_restr	0.055
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.957
r_dihedral_angle_3_deg	18.072
r_dihedral_angle_4_deg	15.968
r_dihedral_angle_1_deg	8.426
r_angle_refined_deg	1.154
r_angle_other_deg	0.834
r_chiral_restr	0.055
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Sample
Thermolysin

Specimen Preparation
Sample Aggregation State	3D ARRAY
Vitrification Instrument	HOMEMADE PLUNGER
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details	No reconstruction: diffraction data
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	92
Length b	92
Length c	92
Angle Alpha	120
Angle Beta	90
Angle Gamma	120

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details	Refinement performed with Refmac

Data Acquisition
Detector Type	OTHER
Electron Dose (electrons/Å**2)	5

Imaging Experiment	1	2
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI POLARA 300	FEI TALOS ARCTICA
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	DIFFRACTION	DIFFRACTION
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN	FIELD EMISSION GUN
Acceleration Voltage (kV)	200	200
Imaging Details

EM Software
Task	Software Package	Version
MOLECULAR REPLACEMENT	CCP4 package

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE

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 R01GM133198.