6CLB | pdb_00006clb

3.20 A MicroED structure of proteinase K at 7.8 e- / A^2

ELECTRON CRYSTALLOGRAPHY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CL7	PDB entry 6CL7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.624	α = 90
b = 67.624	β = 90
c = 100.678	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						2016-03-07

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 6CL7	3.2	50.01	2933	210	74.92	0.2215	0.21397	0.32615	RANDOM	51.51

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]
1.36			1.36		-2.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.628
r_dihedral_angle_3_deg	18.804
r_dihedral_angle_4_deg	14.477
r_long_range_B_refined	9.729
r_long_range_B_other	9.727
r_dihedral_angle_1_deg	8.896
r_mcangle_it	4.914
r_mcangle_other	4.912
r_scangle_other	4.879
r_mcbond_other	2.763
r_mcbond_it	2.762
r_scbond_it	2.701
r_scbond_other	2.7
r_angle_refined_deg	1.464
r_angle_other_deg	1.118
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling

Sample
Proteinase K

Specimen Preparation
Sample Aggregation State	3D ARRAY
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)	3.2
Resolution Method	DIFFRACTION PATTERN/LAYERLINES
Other Details
Refinement Type
Symmetry Type	3D CRYSTAL
Space Group Name
Length a	67.6237
Length b	67.6237
Length c	67.6237
Angle Alpha	90
Angle Beta	90
Angle Gamma	90

Map-Model Fitting and Refinement
Id	1 (5I9S)
Refinement Space	RECIPROCAL
Refinement Protocol	OTHER
Refinement Target
Overall B Value	51.51
Fitting Procedure
Details	Electron scattering factors

Data Acquisition
Detector Type	TVIPS TEMCAM-F416 (4k x 4k)
Electron Dose (electrons/Å**2)	0.0357

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TECNAI F20
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	DIFFRACTION
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	EM-Menu	4.0.9.75
MODEL FITTING	MOLREP	11.4.05
MODEL REFINEMENT	REFMAC	5.8.0194
MOLECULAR REPLACEMENT	MOLREP	11.4.05
SYMMETRY DETERMINATION	POINTLESS	1.11.3
CRYSTALLOGRAPHY MERGING	AIMLESS	0.5.32

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