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HRAS A59T GppNHp crystal 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.15 Starting concentration of HRAS A59T GppNHp was 12.1mg/mL in buffer containing 20mM HEPES, 50mM NaCl, 20mM MgCl2 and 1mM DTT at pH 7.5.
Used a 24-well plate sealed with Vaseline and total well volumes of 0.402mL. Hanging drops were 0.001mL mother liquor to 0.001mL protein. Mother liquor contained 3.4mM NaCl, 1mM MgCl2, 15.7mM HEPES (pH7.5), 2.5mM DTT, 10mM Mg(OAc)2, and 44.8% PEG 400.
Crystal Properties Matthews coefficient Solvent content 1.84 33.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.964 α = 90 b = 38.964 β = 90 c = 159.048 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 173.15 IMAGE PLATE RIGAKU RAXIS IV++ 2016-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.32 50 96.7 0.076 0.082 0.031 9.5 6.5 6642
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 2.32 2.36 75.5 0.42 0.516 0.292 0.765 2.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1CTQ 2.322 33.744 16.83 6204 1098 86.19 0.1868 0.1772 0.1787 0.2635 0.2658 random selection 29.9626
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 10.472 f_angle_d 0.916 f_chiral_restr 0.047 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1278 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHENIX phasing