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OrfE-CoA-glycylthricin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MES pH 6.5
0.2 M ammonium sulfate
12.5 % PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.94 58.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.358 α = 90 b = 102.791 β = 90 c = 386.422 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2021-10-05 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) 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 2.357 30 99.7 0.05 0.061 39.4 10.2 87496
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.36 2.44 98.9 0.352 0.394 6.5
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 3PP9 2.357 29.778 87239 4259 99.477 0.224 0.223 0.2276 0.2404 0.2444 33.296
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] -0.009 0.006 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.256 r_dihedral_angle_3_deg 16.341 r_dihedral_angle_4_deg 15.961 r_dihedral_angle_1_deg 6.234 r_lrange_it 6.02 r_lrange_other 6.015 r_scangle_it 3.953 r_scangle_other 3.953 r_mcangle_it 3.582 r_mcangle_other 3.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.256 r_dihedral_angle_3_deg 16.341 r_dihedral_angle_4_deg 15.961 r_dihedral_angle_1_deg 6.234 r_lrange_it 6.02 r_lrange_other 6.015 r_scangle_it 3.953 r_scangle_other 3.953 r_mcangle_it 3.582 r_mcangle_other 3.581 r_scbond_it 2.437 r_scbond_other 2.437 r_mcbond_it 2.161 r_mcbond_other 2.161 r_angle_refined_deg 1.42 r_angle_other_deg 1.244 r_nbd_other 0.292 r_symmetry_nbd_refined 0.288 r_symmetry_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.184 r_nbd_refined 0.182 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.151 r_ncsr_local_group_25 0.079 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_15 0.077 r_ncsr_local_group_4 0.076 r_ncsr_local_group_19 0.076 r_ncsr_local_group_5 0.075 r_ncsr_local_group_10 0.074 r_ncsr_local_group_3 0.071 r_ncsr_local_group_27 0.071 r_ncsr_local_group_7 0.07 r_ncsr_local_group_1 0.069 r_ncsr_local_group_23 0.069 r_ncsr_local_group_14 0.067 r_ncsr_local_group_20 0.067 r_ncsr_local_group_18 0.066 r_ncsr_local_group_28 0.066 r_ncsr_local_group_21 0.065 r_ncsr_local_group_24 0.065 r_symmetry_xyhbond_nbd_other 0.064 r_ncsr_local_group_13 0.064 r_ncsr_local_group_26 0.064 r_ncsr_local_group_11 0.062 r_ncsr_local_group_16 0.062 r_ncsr_local_group_12 0.06 r_chiral_restr 0.059 r_ncsr_local_group_8 0.059 r_ncsr_local_group_22 0.059 r_ncsr_local_group_6 0.053 r_ncsr_local_group_9 0.053 r_ncsr_local_group_2 0.051 r_ncsr_local_group_17 0.035 r_bond_refined_d 0.006 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 9937 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 450
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing