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CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN COMPLEX WITH GDP (2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q21 PDB ENTRY 4Q21
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291.15 PROTEIN SOLUTION: 13.35 MG/ML PROTEIN, 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM SODIUM AZIDE; RESERVOIR SOLUTION: 100 MM HEPES PH 7.2, 200 MM MAGNESIUM ACETATE, 16% 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 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.41 α = 90 b = 69.41 β = 90 c = 34.76 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 2004-12-01 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 1.22 69.34 94.1 0.05 21.5 6.09 47013
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 1.22 1.25 55.5 0.46 3 4.21
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 4Q21 1.22 69.34 44702 2294 94.1 0.15 0.149 0.2101 0.176 0.2449 RANDOM 17.04
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] -0.96 -0.96 1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.221 r_dihedral_angle_4_deg 18.41 r_dihedral_angle_3_deg 14.017 r_dihedral_angle_1_deg 6.437 r_scangle_it 2.622 r_scbond_it 1.93 r_angle_refined_deg 1.534 r_mcangle_it 1.183 r_mcbond_it 1.089 r_angle_other_deg 0.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.221 r_dihedral_angle_4_deg 18.41 r_dihedral_angle_3_deg 14.017 r_dihedral_angle_1_deg 6.437 r_scangle_it 2.622 r_scbond_it 1.93 r_angle_refined_deg 1.534 r_mcangle_it 1.183 r_mcbond_it 1.089 r_angle_other_deg 0.813 r_symmetry_vdw_other 0.289 r_xyhbond_nbd_refined 0.246 r_nbd_refined 0.245 r_symmetry_hbond_refined 0.193 r_nbd_other 0.183 r_symmetry_vdw_refined 0.182 r_nbtor_refined 0.179 r_nbtor_other 0.08 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 1294 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing