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Crystal structure of HRAS(G12V) - anti-RAS Fv complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AGP PDB ENTRY 1AGP, 1A2Y experimental model PDB 1A2Y PDB ENTRY 1AGP, 1A2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 PROTEIN WAS CRYSTALLIZED FROM 17-18 % PEG3350, 400 MM ZINC ACETATE, 100 MM SODIUM CACODYLATE, PH 5.8, 0.03 % DICHLOROMETHANE
Crystal Properties Matthews coefficient Solvent content 2.15 38.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.528 α = 90 b = 84.632 β = 90 c = 62.592 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 CCD 2005-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 50.32 98.2 0.1 10.42 3.38 27214 3.7
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 2 2.02 97.2 0.36 2.67 3.35
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1AGP, 1A2Y 2 41.89 25816 1369 97.9 0.198 0.194 0.271 RANDOM 24.27
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 36.865 r_dihedral_angle_4_deg 20.435 r_dihedral_angle_3_deg 16.388 r_dihedral_angle_1_deg 6.885 r_scangle_it 4.154 r_scbond_it 2.87 r_angle_refined_deg 1.812 r_mcangle_it 1.796 r_mcbond_it 1.183 r_symmetry_hbond_refined 0.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.865 r_dihedral_angle_4_deg 20.435 r_dihedral_angle_3_deg 16.388 r_dihedral_angle_1_deg 6.885 r_scangle_it 4.154 r_scbond_it 2.87 r_angle_refined_deg 1.812 r_mcangle_it 1.796 r_mcbond_it 1.183 r_symmetry_hbond_refined 0.419 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.283 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.2 r_chiral_restr 0.142 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3003 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction TRUNCATE data scaling AMoRE phasing