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Structure of apo human Nek7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W5B PDB ENTRY 2W5B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 100 MM HEPES, PH 7.5, 15% PEG 5000 MME, 400 MM AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.89 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.937 α = 90 b = 132.322 β = 90 c = 133.366 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 66.2 96.9 0.07 12.5 3.6 23808 2 31.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 98.5 0.28 3.8 3.6
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2W5B 2.1 9.977 0.01 22221 1106 90.73 0.1755 0.1735 0.1804 0.2155 0.2205 45.1
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] -10.4072 -6.517 16.9242
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.637 f_angle_d 1.063 f_chiral_restr 0.072 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2068 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement PHASER phasing