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Crystal structure of the GppNHp-bound H-Ras G60A mutant
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 7 298 PEG 2000 MME, magnesium sulfate, HEPES, hydrogen peroxide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 37.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.292 α = 90 b = 81.419 β = 90 c = 121.302 γ = 90
Symmetry Space Group I 2 2 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 QUANTUM 4 2004-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.0 NSLS X26C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.84 50 97.5 0.087 15.5 4.4 15050 14668 27.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.84 1.92 98.9 0.573 2.9 4.2 1469
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 5P21 1.84 31.61 13925 739 96.55 0.18564 0.18564 0.18279 0.24356 RANDOM 13.592
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] -0.04 0.06 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.852 r_scangle_it 3.935 r_scbond_it 2.401 r_angle_other_deg 1.844 r_mcangle_it 1.563 r_angle_refined_deg 1.557 r_mcbond_it 0.835 r_symmetry_vdw_other 0.288 r_nbd_other 0.241 r_symmetry_vdw_refined 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.852 r_scangle_it 3.935 r_scbond_it 2.401 r_angle_other_deg 1.844 r_mcangle_it 1.563 r_angle_refined_deg 1.557 r_mcbond_it 0.835 r_symmetry_vdw_other 0.288 r_nbd_other 0.241 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.091 r_nbtor_other 0.087 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1368 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing