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The crystal structure of human cdc42 in complex with the CRIB domain of human p21-activated kinase 6 (PAK6)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GRN pdb entry 1GRN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 0.1M acetate, 2M (NH4)2SO4, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.44 64.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.366 α = 90 b = 162.366 β = 90 c = 45.968 γ = 120
Symmetry Space Group P 65 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 MARMOSAIC 225 mm CCD 2006-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 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 2.4 40.59 100 0.071 0.071 14484
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 0.502 0.502
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 1GRN 2.4 40.59 13737 13737 732 99.97 0.20484 0.20484 0.2034 0.2084 0.23184 0.2353 RANDOM 47.158
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] -4.96 -2.48 -4.96 7.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.341 r_dihedral_angle_4_deg 13.291 r_dihedral_angle_3_deg 13.071 r_dihedral_angle_1_deg 6.655 r_scangle_it 1.965 r_angle_refined_deg 1.466 r_scbond_it 1.284 r_angle_other_deg 0.92 r_mcangle_it 0.792 r_mcbond_it 0.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.341 r_dihedral_angle_4_deg 13.291 r_dihedral_angle_3_deg 13.071 r_dihedral_angle_1_deg 6.655 r_scangle_it 1.965 r_angle_refined_deg 1.466 r_scbond_it 1.284 r_angle_other_deg 0.92 r_mcangle_it 0.792 r_mcbond_it 0.496 r_symmetry_vdw_refined 0.247 r_symmetry_vdw_other 0.219 r_nbd_refined 0.201 r_nbd_other 0.182 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.144 r_metal_ion_refined 0.125 r_nbtor_other 0.086 r_mcbond_other 0.083 r_symmetry_hbond_refined 0.081 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 1625 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling PHASER phasing