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Crystal structure of the Rho-GTPase binding domain of YpkA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 276 100mM CAPs pH 10.5, 140mM-180mM NaCl, 16%-18% PEG1500 Micro Seeding, VAPOR DIFFUSION, HANGING DROP, temperature 276K
Crystal Properties Matthews coefficient Solvent content 3.13 60.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.009 α = 90 b = 60.009 β = 90 c = 402.022 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 90 CCD ADSC QUANTUM 315 Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror 2004-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.979 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 99 98.5 0.045 33.1 9 30187
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) 2 2.054 90.29 0.361 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2 33.88 28539 1485 98.5 0.209 0.209 0.208 0.2718 0.237 0.2973 RANDOM 40.659
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] 0.07 0.03 0.07 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.356 r_dihedral_angle_4_deg 17.347 r_dihedral_angle_3_deg 16.453 r_dihedral_angle_1_deg 6.803 r_scangle_it 4.494 r_scbond_it 3.283 r_mcangle_it 1.921 r_angle_refined_deg 1.739 r_mcbond_it 1.664 r_angle_other_deg 0.978
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.356 r_dihedral_angle_4_deg 17.347 r_dihedral_angle_3_deg 16.453 r_dihedral_angle_1_deg 6.803 r_scangle_it 4.494 r_scbond_it 3.283 r_mcangle_it 1.921 r_angle_refined_deg 1.739 r_mcbond_it 1.664 r_angle_other_deg 0.978 r_symmetry_vdw_refined 0.365 r_mcbond_other 0.336 r_symmetry_vdw_other 0.308 r_xyhbond_nbd_other 0.24 r_symmetry_hbond_refined 0.234 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.231 r_nbd_other 0.189 r_nbtor_refined 0.176 r_chiral_restr 0.121 r_nbtor_other 0.089 r_bond_refined_d 0.022 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2169 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing RESOLVE phasing