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Crystal structure of M-Ras P40D in complex with GppNHp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KKQ PDB ENTRY 3KKQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 PEG-1500, magnesium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.96 37.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.72 α = 90 b = 65.705 β = 95.02 c = 74.077 γ = 90
Symmetry Space Group C 1 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 100 CCD ADSC QUANTUM 315 mirrors 2005-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 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 1.35 36.89 94.9 0.045 0.045 11.1 3.7 33462 33462
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 1.35 1.42 92.8 0.268 0.268 2.4 3.7 4768
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3KKQ 1.35 27 31764 31764 1694 94.71 0.18227 0.18227 0.18157 0.1807 0.19514 0.1952 RANDOM 13.573
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 36.643 r_dihedral_angle_4_deg 16.093 r_dihedral_angle_3_deg 10.876 r_dihedral_angle_1_deg 5.497 r_scangle_it 2.572 r_scbond_it 1.622 r_angle_refined_deg 1.22 r_mcangle_it 1.114 r_mcbond_it 0.586 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.643 r_dihedral_angle_4_deg 16.093 r_dihedral_angle_3_deg 10.876 r_dihedral_angle_1_deg 5.497 r_scangle_it 2.572 r_scbond_it 1.622 r_angle_refined_deg 1.22 r_mcangle_it 1.114 r_mcbond_it 0.586 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1370 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 33
Software Software Software Name Purpose BSS data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling