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Orf1-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 3.39 63.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.471 α = 89.753 b = 108.062 β = 90.08 c = 134.557 γ = 96.5
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 2021-03-13 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 1.989 30 97.5 0.037 0.041 0.018 38.1 5.2 388255
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 1.99 2.06 93.2 0.26 0.29 0.127
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7XQA 1.989 27.822 387913 18798 97.476 0.199 0.1979 0.2209 0.2242 29.437
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] -0.086 0.009 0.013 0.134 -0.106 -0.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.112 r_dihedral_angle_4_deg 16.357 r_dihedral_angle_3_deg 15.746 r_dihedral_angle_1_deg 6.611 r_lrange_it 5.783 r_lrange_other 5.679 r_scangle_it 4.041 r_scangle_other 4.041 r_mcangle_it 3.123 r_mcangle_other 3.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.112 r_dihedral_angle_4_deg 16.357 r_dihedral_angle_3_deg 15.746 r_dihedral_angle_1_deg 6.611 r_lrange_it 5.783 r_lrange_other 5.679 r_scangle_it 4.041 r_scangle_other 4.041 r_mcangle_it 3.123 r_mcangle_other 3.123 r_scbond_it 2.558 r_scbond_other 2.558 r_mcbond_it 2.101 r_mcbond_other 2.1 r_angle_refined_deg 1.423 r_angle_other_deg 1.309 r_nbd_other 0.269 r_symmetry_nbd_refined 0.241 r_nbd_refined 0.192 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.145 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_other 0.087 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.069 r_ncsr_local_group_8 0.059 r_ncsr_local_group_15 0.055 r_ncsr_local_group_6 0.054 r_ncsr_local_group_2 0.053 r_ncsr_local_group_14 0.053 r_ncsr_local_group_3 0.052 r_ncsr_local_group_9 0.052 r_ncsr_local_group_13 0.052 r_ncsr_local_group_7 0.051 r_ncsr_local_group_16 0.051 r_ncsr_local_group_18 0.051 r_ncsr_local_group_25 0.051 r_ncsr_local_group_19 0.05 r_ncsr_local_group_21 0.05 r_ncsr_local_group_24 0.05 r_ncsr_local_group_12 0.049 r_ncsr_local_group_10 0.048 r_ncsr_local_group_28 0.048 r_ncsr_local_group_1 0.047 r_ncsr_local_group_23 0.046 r_ncsr_local_group_26 0.046 r_ncsr_local_group_5 0.045 r_ncsr_local_group_27 0.045 r_ncsr_local_group_20 0.044 r_ncsr_local_group_17 0.032 r_ncsr_local_group_11 0.031 r_ncsr_local_group_4 0.027 r_ncsr_local_group_22 0.017 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29166 Nucleic Acid Atoms Solvent Atoms 2426 Heterogen Atoms 704
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing