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CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN COMPLEX WITH GTP (2)
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 7.2 291.15 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 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.32 α = 90 b = 69.32 β = 90 c = 35.01 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 2004-12-07 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 1.3 69.34 100 0.06 16.05 6.27 41195
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 1.3 1.4 100 0.55 3.14 5.5
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 1.3 69.34 39138 2055 100 0.15 0.149 0.2503 0.18 0.2878 RANDOM 13.86
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] -0.99 -0.99 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.894 r_dihedral_angle_4_deg 18.682 r_dihedral_angle_3_deg 14.572 r_dihedral_angle_1_deg 6.807 r_scangle_it 2.808 r_scbond_it 2.028 r_angle_refined_deg 1.753 r_mcangle_it 1.306 r_mcbond_it 1.237 r_angle_other_deg 0.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.894 r_dihedral_angle_4_deg 18.682 r_dihedral_angle_3_deg 14.572 r_dihedral_angle_1_deg 6.807 r_scangle_it 2.808 r_scbond_it 2.028 r_angle_refined_deg 1.753 r_mcangle_it 1.306 r_mcbond_it 1.237 r_angle_other_deg 0.832 r_symmetry_hbond_refined 0.401 r_symmetry_vdw_refined 0.375 r_symmetry_vdw_other 0.373 r_xyhbond_nbd_refined 0.24 r_nbd_refined 0.228 r_nbd_other 0.192 r_nbtor_refined 0.188 r_chiral_restr 0.092 r_nbtor_other 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 199 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing