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Crystal structure of the Grb14 RA and PH domains in complex with GTP-loaded H-Ras
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HK0 PDB ENTRIES 3HK0 (CHAINS A,C,E,G) AND 1LFD (CHAINS B,D,F,H) experimental model PDB 1LFD PDB ENTRIES 3HK0 (CHAINS A,C,E,G) AND 1LFD (CHAINS B,D,F,H)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 315 14% (w/v) PEG 3350, 100 mM MES, pH 5.9, 200 mM MgCl2, 2% glycerol, and 3% glucose, VAPOR DIFFUSION, HANGING DROP, temperature 315K
Crystal Properties Matthews coefficient Solvent content 2.39 48.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.727 α = 90 b = 115.593 β = 96.75 c = 103.107 γ = 90
Symmetry Space Group P 1 21 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 2011-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.000 NSLS X25
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 2.4 50 99.9 0.058 23.8 3.7 71989
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 3HK0 (CHAINS A,C,E,G) AND 1LFD (CHAINS B,D,F,H) 2.4 50 68338 3628 99.65 0.22149 0.21853 0.2769 0.279 RANDOM 66.457
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] 1.97 0.8 0.69 -2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.702 r_dihedral_angle_4_deg 17.731 r_dihedral_angle_3_deg 16.15 r_dihedral_angle_1_deg 6.046 r_angle_refined_deg 1.233 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.702 r_dihedral_angle_4_deg 17.731 r_dihedral_angle_3_deg 16.15 r_dihedral_angle_1_deg 6.046 r_angle_refined_deg 1.233 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13500 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 186
Software Software Software Name Purpose REFMAC refinement