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GPN-loop GTPase from Sulfolobus acidocaldarius closed state (GppNHp)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YR7 1YR7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 0.018 M CaCl2, 0.09M Sodium acetate pH=4.6, 27% (v/v) MPD, 10% (v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.305 α = 90 b = 84.95 β = 95.618 c = 75.322 γ = 90
Symmetry Space Group I 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 EIGER X 16M flexible two-stage focusing X-ray optics 2020-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.8 41.09 90.1 0.029 0.038 0.027 0.999 9.1 3.5 24163 41.25
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 1.8 1.84 54.9 0.421 0.573 0.385 0.92 2.2 3.5
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 FREE R-VALUE 1YR7 1.8 41.09 1.35 24081 795 89.53 0.1735 0.1725 0.1733 0.204 0.2051 70.72
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 13.9358 f_angle_d 0.812 f_chiral_restr 0.0536 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1961 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement xia2 data scaling BALBES phasing xia2 data reduction ARP/wARP model building