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3D electron diffraction structure of thermolysin from Bacillus thermoproteolyticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FJ3
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.2267 0.2923 0.2962 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
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