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CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN COMPLEX WITH S-caged GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5P21 PDB ENTRY 5P21
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 291.15 PROTEIN SOLUTION: 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM SODIUM AZIDE; RESERVOIR SOLUTION: 100 MM HEPES PH 7.4, 200 MM MAGNESIUM ACETATE, 17% PEG 8000 (FRESHLY PREPARED) MIXTURE OF EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTION, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K
Crystal Properties Matthews coefficient Solvent content 2.2 44.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.097 α = 90 b = 69.097 β = 90 c = 35.465 γ = 90
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 2003-11-17 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 1.24 69.01 96.8 0.05 33.4 6.87 46194
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 1.24 1.26 70.7 0.33 3.1 2.68
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 5P21 1.24 69.01 44152 2042 96.8 0.148 0.146 0.2451 0.186 0.2771 RANDOM 14.2
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] -0.41 -0.41 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.882 r_dihedral_angle_4_deg 17.487 r_dihedral_angle_3_deg 14.428 r_dihedral_angle_1_deg 6.657 r_scangle_it 2.458 r_scbond_it 1.782 r_angle_refined_deg 1.625 r_mcangle_it 1.158 r_mcbond_it 1.001 r_angle_other_deg 0.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.882 r_dihedral_angle_4_deg 17.487 r_dihedral_angle_3_deg 14.428 r_dihedral_angle_1_deg 6.657 r_scangle_it 2.458 r_scbond_it 1.782 r_angle_refined_deg 1.625 r_mcangle_it 1.158 r_mcbond_it 1.001 r_angle_other_deg 0.803 r_symmetry_hbond_refined 0.411 r_symmetry_vdw_refined 0.344 r_symmetry_vdw_other 0.281 r_xyhbond_nbd_refined 0.249 r_nbd_refined 0.226 r_nbtor_refined 0.188 r_nbd_other 0.18 r_nbtor_other 0.087 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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_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 1317 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement MOLREP phasing