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Human NDPK-C in complex with UDP 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 2.46 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.532 α = 90 b = 115.991 β = 93.281 c = 83.842 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 EIGER2 X CdTe 16M Toroidal mirror 2021-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.6888 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 1.87 47.717 99.9 0.042 0.047 0.02 0.997 15 5.2 83689 44
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 1.87 1.94 99.5 1.187 1.331 0.592 0.697 1.1 4.9
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 FOURIER SYNTHESIS FREE R-VALUE 1.87 47.717 83594 2091 99.722 0.171 0.1704 0.1814 0.2026 0.2094 58.175
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] 0.04 2.016 -0.875 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.211 r_dihedral_angle_6_deg 14.884 r_dihedral_angle_2_deg 10.638 r_lrange_other 9.092 r_lrange_it 9.083 r_scangle_it 7.505 r_scangle_other 7.504 r_dihedral_angle_1_deg 6.499 r_scbond_other 5.254 r_scbond_it 5.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.211 r_dihedral_angle_6_deg 14.884 r_dihedral_angle_2_deg 10.638 r_lrange_other 9.092 r_lrange_it 9.083 r_scangle_it 7.505 r_scangle_other 7.504 r_dihedral_angle_1_deg 6.499 r_scbond_other 5.254 r_scbond_it 5.251 r_mcangle_it 4.56 r_mcangle_other 4.531 r_mcbond_it 3.548 r_mcbond_other 3.544 r_angle_refined_deg 1.618 r_angle_other_deg 0.514 r_nbd_refined 0.217 r_symmetry_nbd_other 0.19 r_nbd_other 0.184 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.176 r_xyhbond_nbd_refined 0.166 r_symmetry_nbd_refined 0.16 r_symmetry_xyhbond_nbd_other 0.129 r_metal_ion_refined 0.087 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_7 0.081 r_ncsr_local_group_5 0.079 r_ncsr_local_group_2 0.076 r_ncsr_local_group_1 0.075 r_ncsr_local_group_11 0.075 r_ncsr_local_group_13 0.075 r_chiral_restr 0.074 r_ncsr_local_group_8 0.073 r_ncsr_local_group_3 0.072 r_ncsr_local_group_4 0.072 r_ncsr_local_group_10 0.072 r_ncsr_local_group_12 0.072 r_ncsr_local_group_14 0.066 r_ncsr_local_group_6 0.064 r_ncsr_local_group_9 0.064 r_ncsr_local_group_15 0.056 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 313 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing