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Structure of Bacillus pumilus catalase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.1 M sodium acetate, 50 mM NaCl, 10 mM CoCl2, 12-20% 2-methyl-2,4-pentanediol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.647 α = 90 b = 109.191 β = 91.67 c = 102.829 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD 2013-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.98 CLSI 08ID-1
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 1.65 102.79 96.7 0.068 10 2.8 233888 233888 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 95.9 0.414 0.414 1.8 2.8 33855
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1QWL 1.65 102.79 233888 233679 11569 96.36 0.1723 0.1709 0.181 0.1992 0.2073 RANDOM 20.008
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] -1.07 0.14 0.88 0.17
RMS Deviations Key Refinement Restraint Deviation r_mcangle_it 1.847 r_angle_refined_deg 1.766 r_angle_other_deg 1.436 r_mcbond_it 1.331 r_mcbond_other 1.327 r_chiral_restr 0.122 r_bond_refined_d 0.018 r_gen_planes_refined 0.014 r_bond_other_d 0.009 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15680 Nucleic Acid Atoms Solvent Atoms 1751 Heterogen Atoms 368
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data scaling XDS data reduction MOLREP phasing