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GTPase HRAS mutant D33K under ambient 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 1.96 37.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.787 α = 90 b = 39.787 β = 90 c = 161.7 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 CCD MAR CCD 165 mm 2016-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID27 0.374 ESRF ID27
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 1.95 34.457 87.9 0.144 8.8 5.8 9920
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 1.95 2.06 88.7 0.846 0.846 0.8 5.8
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 1.95 20 9419 488 85.7 0.184 0.181 0.1913 0.25 0.2561 RANDOM 27.67
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] -0.28 -0.14 -0.28 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.516 r_dihedral_angle_4_deg 21.105 r_dihedral_angle_3_deg 17.066 r_dihedral_angle_1_deg 6.915 r_angle_refined_deg 1.842 r_angle_other_deg 1.165 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.516 r_dihedral_angle_4_deg 21.105 r_dihedral_angle_3_deg 17.066 r_dihedral_angle_1_deg 6.915 r_angle_refined_deg 1.842 r_angle_other_deg 1.165 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 82 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction