☰ Navigation Tabs
Crystal structure of adenosylcobinamide kinase / adenosylcobinamide phosphate guanylyltransferase from Methylocapsa palsarum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C9K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.09 M NPS (sodium nitrate, sodium phosphate dibasic, ammonium sulfate), 0.1 M Buffer System 3 (Tris, Bicine (pH 8.5)), and 37.5% of Precipitant Mix 4 (25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350)
Crystal Properties Matthews coefficient Solvent content 2.76 55.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.6 α = 90 b = 104.97 β = 90 c = 111.5 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 PIXEL DECTRIS EIGER X 9M 2022-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1 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 1.8 29.654 99.8 0.05 1 26.1 13.3 57890
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 1.8 1.84 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 1.8 29.654 57890 2794 99.709 0.223 0.2218 0.2266 0.2565 0.2631 41.419
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] -0.002 0.003 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.377 r_dihedral_angle_4_deg 18.504 r_dihedral_angle_3_deg 15.175 r_lrange_other 7.984 r_lrange_it 7.975 r_dihedral_angle_1_deg 7.163 r_scangle_other 6.314 r_scangle_it 6.31 r_mcangle_it 4.885 r_mcangle_other 4.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.377 r_dihedral_angle_4_deg 18.504 r_dihedral_angle_3_deg 15.175 r_lrange_other 7.984 r_lrange_it 7.975 r_dihedral_angle_1_deg 7.163 r_scangle_other 6.314 r_scangle_it 6.31 r_mcangle_it 4.885 r_mcangle_other 4.885 r_scbond_it 4.294 r_scbond_other 4.291 r_mcbond_it 3.491 r_mcbond_other 3.491 r_angle_refined_deg 1.555 r_angle_other_deg 1.308 r_xyhbond_nbd_other 0.214 r_nbd_other 0.212 r_nbd_refined 0.202 r_symmetry_nbd_other 0.192 r_symmetry_xyhbond_nbd_refined 0.187 r_symmetry_nbd_refined 0.168 r_nbtor_refined 0.153 r_xyhbond_nbd_refined 0.142 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.014 r_bond_refined_d 0.009 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 3721 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing