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Crystal Structure of DiRas2 in Complex With GDP and Inorganic Phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KAO PDB Entry: 1KAO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 25% PEG 3350; 0.20M Sodium Chloride; 0.1M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.041 α = 90 b = 74.931 β = 90 c = 85.691 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 MARRESEARCH 2005-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.98400 SLS X10SA
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 1.65 46.32 99.3 0.2414 42714 42390
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) 1.65 1.71 98.2 0.232
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: 1KAO 1.65 46.32 42714 40813 2162 99.1 0.16288 0.16288 0.16154 0.1903 0.18797 0.2174 RANDOM 22.85
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] -0.95 -1.5 2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.902 r_dihedral_angle_3_deg 12.187 r_dihedral_angle_4_deg 9.009 r_scangle_it 8.569 r_scbond_it 6.081 r_dihedral_angle_1_deg 5.592 r_mcangle_it 4.359 r_mcbond_it 3.441 r_angle_refined_deg 1.729 r_angle_other_deg 1.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.902 r_dihedral_angle_3_deg 12.187 r_dihedral_angle_4_deg 9.009 r_scangle_it 8.569 r_scbond_it 6.081 r_dihedral_angle_1_deg 5.592 r_mcangle_it 4.359 r_mcbond_it 3.441 r_angle_refined_deg 1.729 r_angle_other_deg 1.168 r_mcbond_other 0.826 r_symmetry_vdw_other 0.295 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.204 r_nbd_other 0.197 r_nbtor_refined 0.178 r_symmetry_hbond_refined 0.177 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.104 r_nbtor_other 0.086 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2543 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing