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The crystal structure of the human Rac GTPase activating protein 1 (RACGAP1) MgcRacGAP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F7C PDB entry 1F7C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 25% PEG 3350, 0.1M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 41.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.913 α = 90 b = 53.548 β = 90 c = 67.979 γ = 90
Symmetry Space Group P 21 21 21
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 2006-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00000 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 1.49 42.07 99.9 0.075 0.075 7 32274 32274
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 1.49 1.54 99.3 0.491 5.5 3134
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 (All) 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 1F7C 1.49 42.07 30586 30586 1631 99.85 0.15307 0.15307 0.15188 0.1514 0.17611 0.1791 RANDOM 11.767
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 0.16 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.956 r_dihedral_angle_4_deg 16.415 r_dihedral_angle_3_deg 11.969 r_dihedral_angle_1_deg 11.518 r_scangle_it 5.705 r_scbond_it 3.928 r_mcangle_it 2.912 r_mcbond_it 2.183 r_angle_refined_deg 1.703 r_angle_other_deg 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.956 r_dihedral_angle_4_deg 16.415 r_dihedral_angle_3_deg 11.969 r_dihedral_angle_1_deg 11.518 r_scangle_it 5.705 r_scbond_it 3.928 r_mcangle_it 2.912 r_mcbond_it 2.183 r_angle_refined_deg 1.703 r_angle_other_deg 1.05 r_mcbond_other 0.578 r_symmetry_vdw_other 0.27 r_symmetry_vdw_refined 0.255 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.202 r_nbd_other 0.196 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.156 r_chiral_restr 0.112 r_nbtor_other 0.088 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1562 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing