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E426Q-glycine-glycylthricin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XQA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1 M Tris-HCl pH8.5, 0.2 M KBr, 8 % PEG 550 MME and 8 % PEG 20000
Crystal Properties Matthews coefficient Solvent content 3.38 63.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.375 α = 89.976 b = 107.369 β = 89.994 c = 135.041 γ = 83.606
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RAYONIX MX300-HS 2021-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.099 30 98.2 0.054 0.06 0.027 29.6 4.9 330834
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 97.1 0.661 0.742 0.336 2.4 4.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7XQA 2.099 28.114 319322 15925 94.694 0.198 0.1969 0.203 0.2226 0.2263 31.774
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] -0.109 -0.13 -0.084 0.251 0.101 -0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.006 r_dihedral_angle_3_deg 15.99 r_dihedral_angle_4_deg 15.522 r_dihedral_angle_1_deg 6.596 r_lrange_it 6.108 r_lrange_other 6.108 r_scangle_it 4.021 r_scangle_other 4.021 r_mcangle_it 3.149 r_mcangle_other 3.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.006 r_dihedral_angle_3_deg 15.99 r_dihedral_angle_4_deg 15.522 r_dihedral_angle_1_deg 6.596 r_lrange_it 6.108 r_lrange_other 6.108 r_scangle_it 4.021 r_scangle_other 4.021 r_mcangle_it 3.149 r_mcangle_other 3.149 r_scbond_it 2.468 r_scbond_other 2.468 r_mcbond_it 1.995 r_mcbond_other 1.995 r_angle_refined_deg 1.376 r_angle_other_deg 1.251 r_nbd_other 0.283 r_symmetry_nbd_refined 0.256 r_nbd_refined 0.188 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.152 r_xyhbond_nbd_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.136 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.064 r_ncsr_local_group_6 0.055 r_ncsr_local_group_2 0.052 r_ncsr_local_group_15 0.052 r_ncsr_local_group_24 0.052 r_ncsr_local_group_16 0.046 r_ncsr_local_group_3 0.045 r_ncsr_local_group_7 0.045 r_ncsr_local_group_12 0.045 r_ncsr_local_group_8 0.044 r_ncsr_local_group_10 0.044 r_ncsr_local_group_18 0.044 r_ncsr_local_group_26 0.044 r_ncsr_local_group_5 0.043 r_ncsr_local_group_14 0.043 r_ncsr_local_group_21 0.043 r_ncsr_local_group_28 0.043 r_ncsr_local_group_1 0.042 r_ncsr_local_group_19 0.042 r_ncsr_local_group_25 0.042 r_ncsr_local_group_9 0.041 r_ncsr_local_group_13 0.041 r_ncsr_local_group_23 0.041 r_ncsr_local_group_20 0.038 r_ncsr_local_group_27 0.038 r_symmetry_xyhbond_nbd_other 0.037 r_ncsr_local_group_17 0.029 r_ncsr_local_group_4 0.022 r_ncsr_local_group_22 0.018 r_ncsr_local_group_11 0.015 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29184 Nucleic Acid Atoms Solvent Atoms 2548 Heterogen Atoms 704
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing