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Crystal structure of M-Ras P40D in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X1R PDB ENTRY 1X1R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 PEG-4000, sodium acetate, ammonium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.947 α = 90 b = 70.754 β = 90 c = 43.445 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC QUANTUM 315 mirrors 2005-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.8 SPring-8 BL41XU
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 1.2 36.11 98.4 0.06 0.06 8.4 7.1 62215 62215
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 1.2 1.26 97.3 0.286 0.286 2.6 7.1 8859
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1X1R 1.2 29.51 59019 59019 3159 98.18 0.17658 0.17658 0.17576 0.1763 0.19222 0.1911 RANDOM 10.329
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 36.544 r_dihedral_angle_4_deg 16.952 r_dihedral_angle_3_deg 11.436 r_dihedral_angle_1_deg 5.425 r_scangle_it 2.137 r_scbond_it 1.457 r_angle_refined_deg 1.161 r_mcangle_it 0.991 r_mcbond_it 0.61 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.544 r_dihedral_angle_4_deg 16.952 r_dihedral_angle_3_deg 11.436 r_dihedral_angle_1_deg 5.425 r_scangle_it 2.137 r_scbond_it 1.457 r_angle_refined_deg 1.161 r_mcangle_it 0.991 r_mcbond_it 0.61 r_nbtor_refined 0.311 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.097 r_symmetry_hbond_refined 0.088 r_chiral_restr 0.077 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1387 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 29
Software Software Software Name Purpose BSS data collection CNS refinement REFMAC refinement MOSFLM data reduction SCALA data scaling CNS phasing