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Crystal structure of the human NRAS GTPase bound with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q21 PDB entry 4Q21
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 30.0% PEG 3350, 0.2M Magnesium chloride, 0.1 M Tris-HCl, GDP was added to the concentrated protein to a final concentration of 5mM. Crystallization were set up with 1:100 chymotrypsin, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.78 30.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.061 α = 90 b = 83.061 β = 90 c = 38.907 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS 2008-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.649 40 99.2 0.065 13.9 9.7 18539
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.649 1.71 92.8 0.469 4.6 1710
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 PDB entry 4Q21 1.649 35.967 18528 949 99.16 0.186 0.185 0.1953 0.219 0.2249 RANDOM 19.437
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] -0.056 -0.028 -0.056 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.808 r_dihedral_angle_4_deg 14.187 r_dihedral_angle_3_deg 11.594 r_dihedral_angle_1_deg 5.722 r_scangle_it 3.879 r_mcangle_it 3.021 r_scbond_it 2.846 r_mcbond_it 2.396 r_angle_refined_deg 1.53 r_angle_other_deg 0.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.808 r_dihedral_angle_4_deg 14.187 r_dihedral_angle_3_deg 11.594 r_dihedral_angle_1_deg 5.722 r_scangle_it 3.879 r_mcangle_it 3.021 r_scbond_it 2.846 r_mcbond_it 2.396 r_angle_refined_deg 1.53 r_angle_other_deg 0.943 r_mcbond_other 0.693 r_symmetry_vdw_other 0.26 r_nbd_refined 0.211 r_nbd_other 0.204 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.128 r_symmetry_hbond_refined 0.115 r_xyhbond_nbd_refined 0.108 r_chiral_restr 0.091 r_nbtor_other 0.083 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1216 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 40
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing