☰ Navigation Tabs
Structure of the Rap-RapGAP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SRQ PDB ENTRY 1SRQ for Rap1GAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 285 8-11% PEG 2000 MME, 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 5.061804 75.700363
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.723 α = 90 b = 209.723 β = 90 c = 108.217 γ = 120
Symmetry Space Group P 31 2 1
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 MARMOSAIC 225 mm CCD 2006-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97916 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.4 182.57 99.2 0.087 0.087 15.48 6.5 37639 37639 3 -3
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) 3.4 3.5 98.4 0.335 3.6
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 1SRQ for Rap1GAP 3.4 48.08 37637 35759 1878 99.16 0.23624 0.23389 0.2265 0.28043 0.2698 RANDOM 97.485
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] 4.21 2.1 4.21 -6.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.009 r_dihedral_angle_3_deg 19.627 r_dihedral_angle_4_deg 16.589 r_dihedral_angle_1_deg 6.007 r_angle_refined_deg 1.128 r_scangle_it 0.84 r_mcangle_it 0.798 r_scbond_it 0.485 r_mcbond_it 0.439 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.009 r_dihedral_angle_3_deg 19.627 r_dihedral_angle_4_deg 16.589 r_dihedral_angle_1_deg 6.007 r_angle_refined_deg 1.128 r_scangle_it 0.84 r_mcangle_it 0.798 r_scbond_it 0.485 r_mcbond_it 0.439 r_nbtor_refined 0.305 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.083 r_chiral_restr 0.077 r_metal_ion_refined 0.043 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9422 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 33
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection