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X-ray structure of MNEI mutant Mut9 (E23A, C41A, Y65R, S76Y)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 30-33% PEG4K, 0.1 M sodium acetate buffer pH 4.5 and 0.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.03 39.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.12 α = 90 b = 31.29 β = 108.648 c = 46.1 γ = 90
Symmetry Space Group C 1 2 1
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 2021-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.96 ELETTRA 11.2C
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 1.5 35.58 94.7 0.043 0.052 0.028 0.999 16.3 3.3 27470
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 1.5 1.53 84.6 0.489 0.612 0.36 0.69 2.3 2.8
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 THROUGHOUT 1.55 35.58 26278 1213 98.32 0.223 0.2208 0.2281 0.2747 0.2736 25.562
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] 0.081 0.141 -0.33 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.45 r_dihedral_angle_4_deg 18.573 r_dihedral_angle_3_deg 17.356 r_lrange_it 7.991 r_lrange_other 7.915 r_dihedral_angle_1_deg 7.594 r_scangle_other 4.452 r_scangle_it 4.444 r_mcangle_it 3.802 r_mcangle_other 3.802
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.45 r_dihedral_angle_4_deg 18.573 r_dihedral_angle_3_deg 17.356 r_lrange_it 7.991 r_lrange_other 7.915 r_dihedral_angle_1_deg 7.594 r_scangle_other 4.452 r_scangle_it 4.444 r_mcangle_it 3.802 r_mcangle_other 3.802 r_scbond_it 2.882 r_scbond_other 2.864 r_mcbond_it 2.418 r_mcbond_other 2.418 r_angle_refined_deg 1.625 r_angle_other_deg 1.31 r_symmetry_xyhbond_nbd_refined 0.27 r_xyhbond_nbd_refined 0.222 r_nbd_refined 0.202 r_symmetry_nbd_other 0.199 r_nbd_other 0.188 r_nbtor_refined 0.176 r_ncsr_local_group_1 0.16 r_symmetry_nbd_refined 0.154 r_symmetry_xyhbond_nbd_other 0.09 r_chiral_restr 0.077 r_symmetry_nbtor_other 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1595 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing