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adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase -C91S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8YEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 0.49M Sodium phosphate monobasic monohydrate, 0.91M Potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 2.1 37.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.97 α = 90 b = 60.97 β = 90 c = 73.392 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2023-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97934 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.5 28.169 100 0.05 1 33.6 20.3 24858
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.5 28.169 24834 1273 99.968 0.207 0.2049 0.2143 0.2389 0.2444 23.346
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] -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.251 r_dihedral_angle_4_deg 14.646 r_dihedral_angle_3_deg 12.342 r_dihedral_angle_1_deg 6.365 r_lrange_it 5.857 r_lrange_other 5.85 r_scangle_other 4.559 r_scangle_it 4.541 r_scbond_other 3.241 r_scbond_it 3.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.251 r_dihedral_angle_4_deg 14.646 r_dihedral_angle_3_deg 12.342 r_dihedral_angle_1_deg 6.365 r_lrange_it 5.857 r_lrange_other 5.85 r_scangle_other 4.559 r_scangle_it 4.541 r_scbond_other 3.241 r_scbond_it 3.228 r_mcangle_other 2.738 r_mcangle_it 2.737 r_mcbond_it 1.988 r_mcbond_other 1.977 r_angle_refined_deg 1.905 r_angle_other_deg 1.541 r_symmetry_nbd_refined 0.269 r_nbd_other 0.23 r_nbd_refined 0.225 r_symmetry_xyhbond_nbd_refined 0.216 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1316 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing