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Human NDPK-C in complex with ADP and Mg2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Structure of ADP complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 27% glycerol, 7% PEG 8000, 40 mM KH2PO4
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.46 α = 90 b = 116.31 β = 93.054 c = 84.07 γ = 90
Symmetry Space Group C 1 2 1
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 X 2M KB mirror 2021-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.1 42.011 95.8 0.184 0.199 0.995 10.01 6.6 57087 41.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 73.1 1.509 1.659 0.466 1.72 5.9
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 2.1 42.011 57087 2382 95.821 0.174 0.1722 0.1823 0.2045 0.2098 39.151
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] 0.344 0.735 -0.853 0.429
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.973 r_dihedral_angle_6_deg 15.579 r_dihedral_angle_2_deg 10.875 r_lrange_it 7.94 r_lrange_other 7.927 r_scangle_other 6.526 r_scangle_it 6.525 r_dihedral_angle_1_deg 6.469 r_scbond_it 4.283 r_scbond_other 4.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.973 r_dihedral_angle_6_deg 15.579 r_dihedral_angle_2_deg 10.875 r_lrange_it 7.94 r_lrange_other 7.927 r_scangle_other 6.526 r_scangle_it 6.525 r_dihedral_angle_1_deg 6.469 r_scbond_it 4.283 r_scbond_other 4.283 r_mcangle_it 3.737 r_mcangle_other 3.718 r_mcbond_it 2.654 r_mcbond_other 2.653 r_angle_refined_deg 1.641 r_angle_other_deg 0.516 r_nbd_refined 0.217 r_symmetry_nbd_refined 0.203 r_nbd_other 0.198 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.164 r_dihedral_angle_other_2_deg 0.131 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_refined 0.075 r_ncsr_local_group_4 0.075 r_ncsr_local_group_2 0.074 r_ncsr_local_group_11 0.073 r_ncsr_local_group_5 0.072 r_ncsr_local_group_7 0.072 r_ncsr_local_group_1 0.071 r_ncsr_local_group_13 0.071 r_ncsr_local_group_3 0.07 r_ncsr_local_group_8 0.07 r_ncsr_local_group_10 0.07 r_ncsr_local_group_12 0.069 r_ncsr_local_group_14 0.066 r_ncsr_local_group_6 0.064 r_ncsr_local_group_9 0.062 r_metal_ion_refined 0.061 r_ncsr_local_group_15 0.051 r_symmetry_xyhbond_nbd_other 0.049 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 7284 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing