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Crystal Structure of GTPase Domain of Human Septin 12 in complex with GMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z51
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.1 M bicine/Trizma base pH 8.5, 20mM of each: 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol
Crystal Properties Matthews coefficient Solvent content 2.06 40.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.511 α = 74.55 b = 70.34 β = 87.84 c = 89.337 γ = 78.1
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 6M 2017-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96861 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.86 46.91 96.4 0.075 0.043 0.992 5.7 1.9 88175 20.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.91 95.2 0.654 0.592 0.572 1.4 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT 4Z51 1.86 46.91 1.96 86997 4223 94.89 0.1941 0.1921 0.1935 0.233 0.2338 32.2296
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.414 f_angle_d 0.571 f_chiral_restr 0.044 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8551 Nucleic Acid Atoms Solvent Atoms 793 Heterogen Atoms 132
Software Software Software Name Purpose xia2 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction xia2 data reduction