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Structure of ClpP from Bacillus subtilis in complex with DFP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KTG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 5.6 295 0.1M bicine/Trizma base(pH 8.5), 0.03M magnesium chloride, 0.03M calcium chloride, 10%(w/v) PEG 4000, 20%(v/v) glycerol, hanging drop, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.09 60.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.337 α = 90 b = 152 β = 113.21 c = 110.067 γ = 90
Symmetry Space Group C 1 2 1
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 BRUKER SMART 6500 2011-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.55 50 88.3 0.063 19 3 52595 52506
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 2.55 2.59 83 0.455 2.3 2446
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3KTG 2.558 37.119 1.35 54137 51513 2624 86.53 0.2195 0.2195 0.2162 0.2125 0.28 0.2771 RANDOM 42.5829
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] 1.8465 0.2201 1.0462 -2.8926
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.094 f_angle_d 1.324 f_chiral_restr 0.083 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9576 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection MOLREP phasing