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Orf1-glycine-4-aminobutylthricin 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 3.4 63.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.644 α = 89.963 b = 107.875 β = 90.132 c = 134.782 γ = 83.438
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 2022-03-11 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 2.119 30 98.2 0.047 0.053 0.025 30 4.6 322706
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 2.12 2.2 97.1 0.6 0.68 0.32 2.5 4.5
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 2.119 29.393 318833 16133 96.761 0.196 0.1946 0.2015 0.2148 0.2031 31.025
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] -0.129 0.032 -0.005 0.112 0.082 0.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.404 r_dihedral_angle_3_deg 15.58 r_dihedral_angle_4_deg 13.409 r_dihedral_angle_1_deg 6.813 r_lrange_it 6.668 r_lrange_other 6.668 r_scangle_it 4.488 r_scangle_other 4.488 r_mcangle_it 3.339 r_mcangle_other 3.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.404 r_dihedral_angle_3_deg 15.58 r_dihedral_angle_4_deg 13.409 r_dihedral_angle_1_deg 6.813 r_lrange_it 6.668 r_lrange_other 6.668 r_scangle_it 4.488 r_scangle_other 4.488 r_mcangle_it 3.339 r_mcangle_other 3.338 r_scbond_it 2.838 r_scbond_other 2.838 r_mcbond_it 2.185 r_mcbond_other 2.184 r_angle_refined_deg 1.41 r_angle_other_deg 1.309 r_nbd_other 0.246 r_nbd_refined 0.191 r_symmetry_nbd_other 0.19 r_symmetry_nbd_refined 0.174 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_28 0.073 r_ncsr_local_group_18 0.072 r_chiral_restr 0.067 r_ncsr_local_group_6 0.065 r_ncsr_local_group_21 0.064 r_ncsr_local_group_24 0.064 r_ncsr_local_group_2 0.062 r_ncsr_local_group_12 0.062 r_ncsr_local_group_14 0.062 r_ncsr_local_group_15 0.062 r_ncsr_local_group_26 0.062 r_ncsr_local_group_8 0.06 r_ncsr_local_group_16 0.06 r_ncsr_local_group_3 0.052 r_ncsr_local_group_9 0.051 r_ncsr_local_group_19 0.051 r_ncsr_local_group_20 0.051 r_ncsr_local_group_7 0.05 r_ncsr_local_group_1 0.049 r_ncsr_local_group_10 0.049 r_ncsr_local_group_13 0.049 r_ncsr_local_group_25 0.049 r_ncsr_local_group_27 0.049 r_ncsr_local_group_5 0.048 r_ncsr_local_group_23 0.048 r_symmetry_xyhbond_nbd_other 0.037 r_ncsr_local_group_17 0.027 r_ncsr_local_group_22 0.02 r_ncsr_local_group_4 0.015 r_ncsr_local_group_11 0.01 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28839 Nucleic Acid Atoms Solvent Atoms 2424 Heterogen Atoms 720
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing