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Co-crystal structure of YpkA-Rac1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H7O PDB ID 2H7O, 1MH1 experimental model PDB 1MH1 PDB ID 2H7O, 1MH1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 100mM HEPES pH 6.5-7.5, 5%-8% PEGMME2000 micro seeding, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.94 68.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.398 α = 92.08 b = 75.519 β = 103.38 c = 99.772 γ = 115.79
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 315 Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror 2005-04-21 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 315 Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror 2005-04-21 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.1 NSLS X29A 2 SYNCHROTRON NSLS BEAMLINE X29A 1.1 NSLS X29A
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 2.6 95.78 99.4 0.09 11.8 3.7 51987
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) 1,2 2.6 2.667 99.5 0.418 3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ID 2H7O, 1MH1 2.6 95.78 51262 2552 99.39 0.224 0.222 0.222 0.2255 0.257 0.2599 RANDOM 62.645
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] 7.3 4.77 -3.29 0.97 -0.77 -5.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.492 r_dihedral_angle_3_deg 19.171 r_dihedral_angle_4_deg 17.951 r_dihedral_angle_1_deg 7.039 r_scangle_it 2.504 r_angle_refined_deg 1.666 r_scbond_it 1.579 r_mcangle_it 1.091 r_mcbond_it 0.874 r_angle_other_deg 0.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.492 r_dihedral_angle_3_deg 19.171 r_dihedral_angle_4_deg 17.951 r_dihedral_angle_1_deg 7.039 r_scangle_it 2.504 r_angle_refined_deg 1.666 r_scbond_it 1.579 r_mcangle_it 1.091 r_mcbond_it 0.874 r_angle_other_deg 0.866 r_nbd_refined 0.242 r_symmetry_vdw_other 0.226 r_symmetry_vdw_refined 0.219 r_xyhbond_nbd_refined 0.196 r_nbtor_refined 0.19 r_nbd_other 0.185 r_symmetry_hbond_refined 0.14 r_mcbond_other 0.136 r_nbtor_other 0.093 r_chiral_restr 0.084 r_xyhbond_nbd_other 0.059 r_metal_ion_refined 0.034 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7058 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing