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Crystal structure of human NEK7 S195D mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DE2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.1 M Tris pH 8.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.84 56.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.601 α = 90 b = 88.601 β = 90 c = 156.088 γ = 120
Symmetry Space Group P 31 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 16M 2022-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953643918037 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.117 44.34 99.5 0.058 1 28.5 20 41004
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.117 2.18 93.6 1.149 0.81
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.12 44.34 39008 1948 99.61 0.1936 0.19117 0.1968 0.24176 0.2463 RANDOM 57.613
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] 0.56 0.28 0.56 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.829 r_dihedral_angle_4_deg 24.038 r_dihedral_angle_3_deg 16.02 r_long_range_B_other 9.013 r_long_range_B_refined 9.012 r_scangle_other 6.991 r_dihedral_angle_1_deg 6.831 r_mcangle_it 5.271 r_mcangle_other 5.27 r_scbond_it 4.671
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.829 r_dihedral_angle_4_deg 24.038 r_dihedral_angle_3_deg 16.02 r_long_range_B_other 9.013 r_long_range_B_refined 9.012 r_scangle_other 6.991 r_dihedral_angle_1_deg 6.831 r_mcangle_it 5.271 r_mcangle_other 5.27 r_scbond_it 4.671 r_scbond_other 4.67 r_mcbond_it 3.871 r_mcbond_other 3.871 r_angle_refined_deg 1.917 r_angle_other_deg 1.419 r_chiral_restr 0.094 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_gen_planes_other 0.005 r_bond_other_d 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4324 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing