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GTPase HRAS under 500 MPa pressure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5P21 PDBID 5P21
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 298 40 mM Tris HCL, 10 mM MgCl2, 2 mM DTE, 26-30 % PEG-400
Crystal Properties Matthews coefficient Solvent content 1.9 35.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.635 α = 90 b = 38.635 β = 90 c = 166.141 γ = 120
Symmetry Space Group P 32 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 293 IMAGE PLATE MAR555 FLAT PANEL 2015-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID09 0.415 ESRF ID09
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.85 55.38 99.9 0.182 4.4 4.9 13092
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.95 100 0.691 0.691 0.9 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDBID 5P21 1.85 20 12380 634 99.5 0.18 0.177 0.1907 0.236 0.2338 RANDOM 24.22
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] -0.07 -0.04 -0.07 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.237 r_dihedral_angle_4_deg 21.074 r_dihedral_angle_3_deg 14.376 r_dihedral_angle_1_deg 6.333 r_angle_refined_deg 1.97 r_angle_other_deg 1.887 r_chiral_restr 0.105 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.237 r_dihedral_angle_4_deg 21.074 r_dihedral_angle_3_deg 14.376 r_dihedral_angle_1_deg 6.333 r_angle_refined_deg 1.97 r_angle_other_deg 1.887 r_chiral_restr 0.105 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1323 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction