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Human NDPK-C in complex with GDP
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 5.4 291 6% PEG 3350, 150 mM Li2SO4, 100 mM Tri-sodium citrate pH 5.4
Crystal Properties Matthews coefficient Solvent content 2.17 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.34 α = 90 b = 78.64 β = 97.561 c = 112.37 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 4M Vertical CRL / horizontal eliptical mirror 2021-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 2.17 46.592 99.5 0.152 0.16 0.998 9.64 10.3 94493 46.2
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 2.17 2.23 94.2 1.388 1.495 0.549 1.04 7.2
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 2.175 46.592 94493 1996 99.551 0.19 0.1888 0.197 0.2289 0.2352 49.233
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] -0.758 -0.311 1.982 -1.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.227 r_dihedral_angle_6_deg 15.36 r_dihedral_angle_2_deg 12.79 r_lrange_other 9.785 r_lrange_it 9.779 r_scangle_it 8.812 r_scangle_other 8.812 r_dihedral_angle_1_deg 6.454 r_scbond_it 6.089 r_scbond_other 6.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.227 r_dihedral_angle_6_deg 15.36 r_dihedral_angle_2_deg 12.79 r_lrange_other 9.785 r_lrange_it 9.779 r_scangle_it 8.812 r_scangle_other 8.812 r_dihedral_angle_1_deg 6.454 r_scbond_it 6.089 r_scbond_other 6.088 r_mcangle_it 4.818 r_mcangle_other 4.818 r_mcbond_it 3.727 r_mcbond_other 3.727 r_angle_refined_deg 1.812 r_angle_other_deg 0.588 r_symmetry_xyhbond_nbd_refined 0.482 r_dihedral_angle_other_2_deg 0.383 r_nbd_other 0.223 r_nbd_refined 0.219 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.181 r_symmetry_xyhbond_nbd_other 0.171 r_symmetry_nbd_refined 0.171 r_ncsr_local_group_43 0.092 r_ncsr_local_group_64 0.091 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.084 r_ncsr_local_group_28 0.084 r_ncsr_local_group_40 0.084 r_ncsr_local_group_4 0.083 r_ncsr_local_group_61 0.082 r_ncsr_local_group_10 0.08 r_ncsr_local_group_22 0.08 r_ncsr_local_group_45 0.08 r_ncsr_local_group_55 0.08 r_ncsr_local_group_31 0.079 r_ncsr_local_group_39 0.079 r_ncsr_local_group_46 0.079 r_ncsr_local_group_49 0.079 r_ncsr_local_group_16 0.078 r_ncsr_local_group_34 0.078 r_ncsr_local_group_57 0.078 r_ncsr_local_group_11 0.077 r_ncsr_local_group_20 0.077 r_ncsr_local_group_25 0.077 r_ncsr_local_group_26 0.077 r_ncsr_local_group_52 0.077 r_ncsr_local_group_54 0.077 r_ncsr_local_group_58 0.077 r_ncsr_local_group_1 0.076 r_ncsr_local_group_5 0.076 r_ncsr_local_group_56 0.076 r_ncsr_local_group_60 0.076 r_ncsr_local_group_66 0.076 r_ncsr_local_group_14 0.075 r_ncsr_local_group_18 0.075 r_ncsr_local_group_19 0.075 r_ncsr_local_group_37 0.075 r_ncsr_local_group_47 0.075 r_ncsr_local_group_50 0.075 r_ncsr_local_group_8 0.074 r_ncsr_local_group_12 0.074 r_ncsr_local_group_15 0.074 r_ncsr_local_group_35 0.074 r_ncsr_local_group_53 0.074 r_ncsr_local_group_13 0.073 r_ncsr_local_group_29 0.073 r_ncsr_local_group_30 0.073 r_ncsr_local_group_7 0.072 r_ncsr_local_group_32 0.072 r_ncsr_local_group_9 0.071 r_ncsr_local_group_17 0.071 r_ncsr_local_group_24 0.071 r_ncsr_local_group_2 0.07 r_ncsr_local_group_33 0.07 r_ncsr_local_group_48 0.069 r_ncsr_local_group_63 0.069 r_ncsr_local_group_3 0.068 r_ncsr_local_group_21 0.068 r_ncsr_local_group_23 0.068 r_ncsr_local_group_59 0.068 r_ncsr_local_group_38 0.067 r_ncsr_local_group_41 0.067 r_ncsr_local_group_36 0.066 r_ncsr_local_group_65 0.066 r_ncsr_local_group_42 0.065 r_ncsr_local_group_51 0.064 r_ncsr_local_group_62 0.062 r_ncsr_local_group_6 0.058 r_ncsr_local_group_44 0.058 r_ncsr_local_group_27 0.056 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14463 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 346
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing