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Human NDPK-C in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZS6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.4 291 6% PEG 3350, 150 mM Li2SO4, 100 mM Tri-sodium citrate pH 5.4
Crystal Properties Matthews coefficient Solvent content 1.89 35.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.315 α = 108.492 b = 67.865 β = 112.343 c = 68.423 γ = 101.105
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-F Toroidal mirror 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0052 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.25 60.12 94.2 0.049 0.06 0.033 0.97 8.6 2.8 198602 12.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.28 89 0.947 1.339 0.947 0.401 0.7 1.8
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 1.255 60.119 198505 2119 94.108 0.147 0.1467 0.1467 0.1755 0.1754 19.87
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] -0.238 -0.167 -0.151 -0.071 -0.243 0.425
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.308 r_lrange_it 16.293 r_lrange_other 15.884 r_dihedral_angle_6_deg 15.609 r_dihedral_angle_3_deg 14.919 r_scangle_it 12.325 r_scangle_other 12.324 r_mcangle_other 8.761 r_mcangle_it 8.76 r_scbond_it 8.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.308 r_lrange_it 16.293 r_lrange_other 15.884 r_dihedral_angle_6_deg 15.609 r_dihedral_angle_3_deg 14.919 r_scangle_it 12.325 r_scangle_other 12.324 r_mcangle_other 8.761 r_mcangle_it 8.76 r_scbond_it 8.6 r_scbond_other 8.6 r_dihedral_angle_1_deg 6.378 r_mcbond_it 6.148 r_mcbond_other 6.127 r_rigid_bond_restr 4.395 r_angle_refined_deg 1.671 r_dihedral_angle_other_2_deg 1.355 r_angle_other_deg 0.916 r_nbd_other 0.41 r_symmetry_nbd_refined 0.389 r_nbd_refined 0.224 r_symmetry_nbd_other 0.208 r_nbtor_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.178 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.057 r_gen_planes_other 0.013 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7253 Nucleic Acid Atoms Solvent Atoms 542 Heterogen Atoms 177
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing