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Crystal structure of glyoxalase/bleomycin resistance protein/dioxygenase from Alicyclobacillus acidocaldarius
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other different crystal form of the same protein that was solved by SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.1 M Bis/Tris propane:NaOH, 2.8 M sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.05 39.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.728 α = 90 b = 104.728 β = 90 c = 49.77 γ = 90
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 QUANTUM 315r mirrors 2011-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97932 APS 19-ID
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 1.5 50 99.6 0.093 32 10 43462 43267 -3 20.1
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 1.5 1.53 99.6 0.827 2.5 7.4 2167
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 (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 THROUGHOUT different crystal form of the same protein that was solved by SAD 1.5 50 43211 42129 1082 99.36 0.13563 0.13563 0.13504 0.1375 0.15911 0.1571 according to the highest possible lattice symmetry 19.261
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] -10.82 -10.82 21.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.072 r_dihedral_angle_4_deg 24.101 r_dihedral_angle_3_deg 13.606 r_dihedral_angle_1_deg 6.603 r_scangle_it 3.515 r_scbond_it 2.227 r_mcangle_it 1.5 r_angle_refined_deg 1.47 r_mcbond_it 0.849 r_angle_other_deg 0.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.072 r_dihedral_angle_4_deg 24.101 r_dihedral_angle_3_deg 13.606 r_dihedral_angle_1_deg 6.603 r_scangle_it 3.515 r_scbond_it 2.227 r_mcangle_it 1.5 r_angle_refined_deg 1.47 r_mcbond_it 0.849 r_angle_other_deg 0.848 r_mcbond_other 0.243 r_chiral_restr 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2288 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 8
Software Software Software Name Purpose SBC-Collect data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling