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Structure of the R178A mutant of delta PDZ DegS protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QF0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 50 mM NaCacodylate pH 6.5, 100 mM NaCitrate, 20% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.216 α = 90 b = 70.216 β = 90 c = 119.228 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 123 IMAGE PLATE RIGAKU RAXIS IV Varimax-HR 2007-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 50 98.2 5938
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 2.7 2.8 87.5 0.201
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2QF0 2.7 29.46 5394 313 89.3 0.249 0.2671 0.262 92.57
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] -30.396 -30.396 60.792
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.01 f_bond_d 0.002 f_bond_d_na f_bond_d_prot f_angle_d f_angle_d_na f_angle_d_prot f_angle_deg f_angle_deg_na f_angle_deg_prot
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.01 f_bond_d 0.002 f_bond_d_na f_bond_d_prot f_angle_d f_angle_d_na f_angle_d_prot f_angle_deg f_angle_deg_na f_angle_deg_prot f_dihedral_angle_d_na f_dihedral_angle_d_prot f_improper_angle_d f_improper_angle_d_na f_improper_angle_d_prot f_mcbond_it f_mcangle_it f_scbond_it f_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1238 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PHASER phasing CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction DENZO data reduction