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Orf1 R342A-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 3.37 63.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.42 α = 90.075 b = 107.933 β = 90.011 c = 133.424 γ = 96.303
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 MX300HE 2022-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
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 2.4 30 98.5 0.06 0.069 0.033 25 4.4 220494
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 2.4 2.49 97.7 0.642 0.729 0.346 2.7 4.3
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 2.4 28.619 212738 10670 94.753 0.201 0.2004 0.2038 0.2204 0.2042 43.163
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] -0.338 0.017 -0.063 0.482 0.018 -0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.295 r_dihedral_angle_3_deg 17.207 r_dihedral_angle_4_deg 15.469 r_lrange_other 8.851 r_lrange_it 8.849 r_dihedral_angle_1_deg 6.65 r_scangle_it 6.645 r_scangle_other 6.645 r_mcangle_it 5.341 r_mcangle_other 5.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.295 r_dihedral_angle_3_deg 17.207 r_dihedral_angle_4_deg 15.469 r_lrange_other 8.851 r_lrange_it 8.849 r_dihedral_angle_1_deg 6.65 r_scangle_it 6.645 r_scangle_other 6.645 r_mcangle_it 5.341 r_mcangle_other 5.341 r_scbond_it 4.232 r_scbond_other 4.232 r_mcbond_it 3.515 r_mcbond_other 3.515 r_angle_refined_deg 1.476 r_angle_other_deg 1.267 r_nbd_other 0.261 r_symmetry_nbd_refined 0.217 r_nbd_refined 0.193 r_symmetry_xyhbond_nbd_other 0.192 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.142 r_xyhbond_nbd_refined 0.141 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_6 0.076 r_ncsr_local_group_24 0.072 r_ncsr_local_group_12 0.068 r_chiral_restr 0.067 r_ncsr_local_group_2 0.066 r_ncsr_local_group_26 0.066 r_ncsr_local_group_15 0.065 r_ncsr_local_group_3 0.061 r_ncsr_local_group_21 0.06 r_ncsr_local_group_7 0.059 r_ncsr_local_group_8 0.059 r_ncsr_local_group_28 0.059 r_ncsr_local_group_9 0.058 r_ncsr_local_group_10 0.058 r_ncsr_local_group_16 0.058 r_ncsr_local_group_14 0.057 r_ncsr_local_group_19 0.057 r_ncsr_local_group_20 0.057 r_ncsr_local_group_5 0.056 r_ncsr_local_group_18 0.056 r_ncsr_local_group_13 0.055 r_ncsr_local_group_25 0.055 r_ncsr_local_group_27 0.055 r_ncsr_local_group_1 0.054 r_ncsr_local_group_23 0.053 r_ncsr_local_group_17 0.038 r_ncsr_local_group_4 0.035 r_ncsr_local_group_11 0.031 r_ncsr_local_group_22 0.022 r_bond_refined_d 0.008 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 29152 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 664
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing