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Fingerprint and Structural Analysis of a Apo SCOR enzyme from Clostridium thermocellum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDE PDB entries 1YDE, 1VL8 experimental model PDB 1VL8 PDB entries 1YDE, 1VL8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 298 25% (w/v) PEG 4000,100mM TAPs pH 9.0, 50mM sodium thiosulfate pentahydrate 1:1 cocktail to protein ratio (10mg/ml), hanging drop vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.86 57.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.287 α = 90 b = 124.287 β = 90 c = 162.608 γ = 90
Symmetry Space Group I 41 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 ADSC Q315 2006-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979454 SSRL BL11-1
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 1.416 99.015 97.7 0.064 18.9 12 68407 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.74
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entries 1YDE, 1VL8 1.698 49.684 1.33 68407 3442 97.69 0.18 0.179 0.1768 0.208 0.2061 32.972
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] -0.339 -0.339 0.677
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.848 f_angle_d 1.327 f_chiral_restr 0.094 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3758 Nucleic Acid Atoms Solvent Atoms 551 Heterogen Atoms 29
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing