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Engineered form of T thermophiles AHIR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.69 54.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.03 α = 90 b = 142.72 β = 90 c = 126.13 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS 6M 2012-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.89 63.06 94.7 0.154 0.177 0.085 0.993 5.6 4 184696
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.92 96.8 1.122 1.298 0.637 0.679 1.5 3.9
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 2 63.06 161433 8715 97.45 0.26 0.2589 0.2616 0.2884 0.2904 46.788
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] 0.829 0.781 -1.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.875 r_dihedral_angle_2_deg 16.468 r_dihedral_angle_6_deg 15.437 r_lrange_other 9.972 r_lrange_it 9.97 r_scangle_it 8.185 r_scangle_other 8.183 r_mcangle_it 6.952 r_mcangle_other 6.952 r_dihedral_angle_1_deg 6.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.875 r_dihedral_angle_2_deg 16.468 r_dihedral_angle_6_deg 15.437 r_lrange_other 9.972 r_lrange_it 9.97 r_scangle_it 8.185 r_scangle_other 8.183 r_mcangle_it 6.952 r_mcangle_other 6.952 r_dihedral_angle_1_deg 6.578 r_scbond_it 5.707 r_scbond_other 5.706 r_mcbond_it 5.117 r_mcbond_other 5.116 r_angle_refined_deg 1.449 r_angle_other_deg 0.481 r_metal_ion_refined 0.231 r_nbd_refined 0.23 r_symmetry_nbd_other 0.191 r_nbd_other 0.185 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.152 r_symmetry_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.105 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.065 r_ncsr_local_group_6 0.032 r_ncsr_local_group_11 0.031 r_ncsr_local_group_10 0.03 r_ncsr_local_group_2 0.028 r_ncsr_local_group_12 0.028 r_ncsr_local_group_7 0.026 r_ncsr_local_group_9 0.025 r_ncsr_local_group_1 0.024 r_ncsr_local_group_4 0.024 r_ncsr_local_group_8 0.024 r_ncsr_local_group_3 0.023 r_ncsr_local_group_13 0.023 r_ncsr_local_group_15 0.023 r_ncsr_local_group_14 0.022 r_ncsr_local_group_5 0.02 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_symmetry_xyhbond_nbd_other 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14460 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing