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Crystal Structure of Bel-1 E166A Mutant.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M imidazole, 0.1M MES monohydrate, 20% ETG, 10% PEG 8000, 0.1M Sodium formate, 0.1M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Potassium sodium tartrate, 0.1M Sodium oxamate
Crystal Properties Matthews coefficient Solvent content 2.71 54.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.498 α = 90 b = 123.498 β = 90 c = 70.644 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL RIGAKU HyPix-6000HE 2023-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.7 27.35 100 0.13 0.14 0.05 0.998 12.2 13.4 67521
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 0.773
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 26.613 67456 3419 99.867 0.164 0.1607 0.1623 0.2253 0.2235 25.914
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] 1.723 0.862 1.723 -5.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.565 r_dihedral_angle_3_deg 15.077 r_dihedral_angle_2_deg 12.175 r_dihedral_angle_1_deg 6.645 r_rigid_bond_restr 6.237 r_lrange_it 5.641 r_lrange_other 5.359 r_scangle_it 4.317 r_scangle_other 4.271 r_mcangle_it 3.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.565 r_dihedral_angle_3_deg 15.077 r_dihedral_angle_2_deg 12.175 r_dihedral_angle_1_deg 6.645 r_rigid_bond_restr 6.237 r_lrange_it 5.641 r_lrange_other 5.359 r_scangle_it 4.317 r_scangle_other 4.271 r_mcangle_it 3.752 r_mcangle_other 3.752 r_scbond_it 3.189 r_scbond_other 3.166 r_mcbond_it 2.747 r_mcbond_other 2.746 r_angle_refined_deg 1.992 r_angle_other_deg 0.673 r_symmetry_xyhbond_nbd_refined 0.442 r_nbd_other 0.301 r_symmetry_nbd_refined 0.299 r_xyhbond_nbd_refined 0.262 r_nbd_refined 0.237 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.186 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.086 r_xyhbond_nbd_other 0.057 r_symmetry_xyhbond_nbd_other 0.02 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4009 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing