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Structure of SlyX protein from Xanthomonas campestris pv. campestris str. ATCC 33913
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.1M Tris pH 8.5, 0.2M Ammonium Sulfate, 20% PEG 3350, 4% Glycerol, 1/60 cymotrypsin, then soaked in
Na Bromide for phasing, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.73 28.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.945 α = 90 b = 35.945 β = 90 c = 81.82 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 100 CCD ADSC QUANTUM 315 2008-02-15 M MAD 2 1 x-ray CCD ADSC QUANTUM 315 2008-04-21 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97931, 0.91966, 0.91948 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 1,2 1.9 50 99.7 0.051 58.469 12.4 4751 4751 -3 34.9
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 1.9 1.94 100 0.533 11.9 298
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2 31.13 4065 4065 191 99.71 0.204 0.204 0.204 0.2108 0.211 0.2269 RANDOM 38.483
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] 1.62 0.81 1.62 -2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.401 r_dihedral_angle_3_deg 18.643 r_dihedral_angle_4_deg 13.087 r_scangle_it 5.167 r_dihedral_angle_1_deg 3.83 r_scbond_it 2.939 r_mcangle_it 1.872 r_angle_refined_deg 1.389 r_angle_other_deg 0.901 r_mcbond_it 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.401 r_dihedral_angle_3_deg 18.643 r_dihedral_angle_4_deg 13.087 r_scangle_it 5.167 r_dihedral_angle_1_deg 3.83 r_scbond_it 2.939 r_mcangle_it 1.872 r_angle_refined_deg 1.389 r_angle_other_deg 0.901 r_mcbond_it 0.88 r_mcbond_other 0.155 r_chiral_restr 0.063 r_bond_refined_d 0.017 r_bond_other_d 0.006 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 404 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building