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Inhibition of Small GTPases by Stabilization of the GDP Complex, a Novel Approach applied to Rit1, a Target for Rheumatoid Arthritis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ERY pdb entry 2ery
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 11-14% w/v PEG4000, 5-8% v/v Jeffamine M600, imidazole , VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.278 α = 90 b = 37.048 β = 95.9 c = 40.736 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 99 CCD Bruker Platinum 135 2007-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.54146
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 2.3 40.5 98 0.0547 36.45 5464 5464
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2ery 2.3 40.5 82115 4860 520 98.57 0.19786 0.18538 0.1924 0.31099 0.3086 RANDOM 15.06
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] 2.07 -0.12 -1.11 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.123 r_dihedral_angle_3_deg 23.608 r_dihedral_angle_4_deg 21.704 r_dihedral_angle_1_deg 12.193 r_scangle_it 4.403 r_scbond_it 3.337 r_angle_refined_deg 3.177 r_mcangle_it 2.063 r_mcbond_it 1.678 r_angle_other_deg 1.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.123 r_dihedral_angle_3_deg 23.608 r_dihedral_angle_4_deg 21.704 r_dihedral_angle_1_deg 12.193 r_scangle_it 4.403 r_scbond_it 3.337 r_angle_refined_deg 3.177 r_mcangle_it 2.063 r_mcbond_it 1.678 r_angle_other_deg 1.567 r_symmetry_hbond_refined 0.446 r_mcbond_other 0.368 r_symmetry_vdw_other 0.36 r_nbd_refined 0.307 r_nbd_other 0.27 r_xyhbond_nbd_refined 0.27 r_symmetry_vdw_refined 0.251 r_nbtor_refined 0.221 r_chiral_restr 0.181 r_nbtor_other 0.108 r_bond_refined_d 0.042 r_gen_planes_refined 0.014 r_xyhbond_nbd_other 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1278 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 29
Software Software Software Name Purpose PROTEUM PLUS data collection Coot model building REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling