☰ Navigation Tabs
The Crystal Structure of human UMP-CMP kinase from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TEV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.5M (NH4)2SO4, 0.1M Tris pH8.5
Crystal Properties Matthews coefficient Solvent content 2.56 56.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.926 α = 90 b = 61.926 β = 90 c = 225.397 γ = 120
Symmetry Space Group P 65 2 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 PILATUS3 S 6M 2020-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 48.473 100 0.075 24 18.1 15960
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 0.937
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 1TEV 2.1 48.473 15874 818 99.987 0.207 0.205 0.2127 0.2497 0.2474 48.109
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] 1.072 0.536 1.072 -3.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.577 r_dihedral_angle_4_deg 18.241 r_dihedral_angle_3_deg 17.218 r_lrange_it 8.935 r_lrange_other 8.9 r_scangle_other 7.913 r_scangle_it 7.904 r_dihedral_angle_1_deg 6.073 r_scbond_it 5.315 r_scbond_other 5.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.577 r_dihedral_angle_4_deg 18.241 r_dihedral_angle_3_deg 17.218 r_lrange_it 8.935 r_lrange_other 8.9 r_scangle_other 7.913 r_scangle_it 7.904 r_dihedral_angle_1_deg 6.073 r_scbond_it 5.315 r_scbond_other 5.314 r_mcangle_it 5.071 r_mcangle_other 5.069 r_mcbond_it 3.973 r_mcbond_other 3.968 r_angle_refined_deg 1.636 r_angle_other_deg 1.401 r_symmetry_nbd_refined 0.27 r_nbd_refined 0.221 r_symmetry_xyhbond_nbd_refined 0.216 r_symmetry_nbd_other 0.175 r_nbd_other 0.175 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.109 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1528 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing