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Crystal structure of M-Ras P40D/D41E/L51R in complex with GppNHp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X1S PDB ENTRY 1X1S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 Ammonium sulfate, sodium acetate, PEG-4000, glycerol, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.196 α = 90 b = 192.248 β = 90 c = 43.235 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU JUPITER 210 mirrors 2008-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 49.57 99.2 0.099 0.099 3.8 6.4 52129 52129
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 1.9 2 94.8 0.282 0.282 2.5 4.1 7118
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1X1S 1.9 49.57 49403 49403 2649 99.18 0.18584 0.18584 0.18392 0.22192 0.2186 RANDOM 24.125
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 r_dihedral_angle_2_deg 39.877 r_dihedral_angle_4_deg 19.483 r_dihedral_angle_3_deg 12.996 r_dihedral_angle_1_deg 5.395 r_scangle_it 2.679 r_scbond_it 1.677 r_angle_refined_deg 1.198 r_mcangle_it 1.157 r_mcbond_it 0.732 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.877 r_dihedral_angle_4_deg 19.483 r_dihedral_angle_3_deg 12.996 r_dihedral_angle_1_deg 5.395 r_scangle_it 2.679 r_scbond_it 1.677 r_angle_refined_deg 1.198 r_mcangle_it 1.157 r_mcbond_it 0.732 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.188 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.078 r_metal_ion_refined 0.039 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4138 Nucleic Acid Atoms Solvent Atoms 415 Heterogen Atoms 114
Software Software Software Name Purpose BSS data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling