☰ Navigation Tabs
Crystal structure of Phosphomevalonate kinase from Silkworm
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 289 1.8 M Ammonium citrate dibasic, 0.1 M Sodium acetate trihydrate pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.27 40.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.07 α = 90 b = 54.07 β = 90 c = 123.12 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS 6M 2019-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
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 1.6 32.48 99.9 0.066 0.068 27.1 23.2 24974
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 99.9 1.236 0.32 15.6
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 3CH4 1.6 32.48 24902 1264 99.872 0.212 0.2097 0.2189 0.2468 0.2532 32.694
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] -0.46 -0.46 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.964 r_dihedral_angle_4_deg 15.851 r_dihedral_angle_3_deg 12.837 r_lrange_other 8.241 r_lrange_it 8.239 r_scangle_it 7.221 r_scangle_other 7.218 r_dihedral_angle_1_deg 6.627 r_scbond_it 4.798 r_scbond_other 4.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.964 r_dihedral_angle_4_deg 15.851 r_dihedral_angle_3_deg 12.837 r_lrange_other 8.241 r_lrange_it 8.239 r_scangle_it 7.221 r_scangle_other 7.218 r_dihedral_angle_1_deg 6.627 r_scbond_it 4.798 r_scbond_other 4.795 r_mcangle_it 3.836 r_mcangle_other 3.834 r_mcbond_it 2.965 r_mcbond_other 2.964 r_angle_other_deg 2.259 r_angle_refined_deg 1.645 r_nbd_other 0.298 r_symmetry_nbd_refined 0.248 r_nbd_refined 0.216 r_symmetry_nbd_other 0.215 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.148 r_xyhbond_nbd_refined 0.096 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.072 r_bond_other_d 0.034 r_gen_planes_other 0.015 r_bond_refined_d 0.012 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1389 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing