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Structure of Rex8A from Paenibacillus barcinonensis complexed with xylose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WU4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 23% PEG 6K, 0.1 M Tris pH 8.0, 0.2 M NaCl, 0.01 M Hexammine cobalt (III) chrloride.
Soaking experiment in the precipitant solution supplemented with 50 mM xylose.
Cryoprotectan solution consisting of mother liquor plus 25% (v/v) glycerol.
Crystal Properties Matthews coefficient Solvent content 2.6 52.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.566 α = 87.83 b = 59.153 β = 77.98 c = 79.534 γ = 74.33
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M KB Mirrors 2015-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.041910 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.93 48.63 96.4 0.125 0.148 0.078 0.992 7.2 3.5 64154
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.98 93.2 0.723 0.879 0.489 0.663 2 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1WU4 1.93 48.63 60880 3260 96.37 0.1909 0.1889 0.1964 0.2286 0.2312 RANDOM 16.208
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] 0.85 1.09 0.4 0.31 -0.74 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.951 r_dihedral_angle_4_deg 15.632 r_dihedral_angle_3_deg 12.641 r_dihedral_angle_1_deg 6.787 r_angle_refined_deg 1.418 r_angle_other_deg 1.362 r_chiral_restr 0.076 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.951 r_dihedral_angle_4_deg 15.632 r_dihedral_angle_3_deg 12.641 r_dihedral_angle_1_deg 6.787 r_angle_refined_deg 1.418 r_angle_other_deg 1.362 r_chiral_restr 0.076 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6226 Nucleic Acid Atoms Solvent Atoms 613 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing