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Structure of L320A mutant 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 7 291 22% PEG 6000, 0.1 M HEPES pH 7, 0.2 M MgCl2, 6% glycerol, 0.01 M Hexammine cobalt (III) chloride. Microseeding. Soaking: 50 mM xylose, 100 mM arabinose. Cryoprotectant solution: mother liquor plus 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.6 52.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.514 α = 87.83 b = 59.172 β = 78.35 c = 79.412 γ = 74.61
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 2016-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979490 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 1.74 57.11 96.6 0.098 0.119 0.067 0.987 7.1 3 87761
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 1.74 1.77 95 0.628 0.759 0.423 0.787 2.1 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 1.74 57.11 83378 4370 96.58 0.2438 0.2421 0.248 0.2773 0.28 RANDOM 14.37
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] 0.98 1.1 0.15 0.12 -0.4 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.386 r_dihedral_angle_3_deg 14.075 r_dihedral_angle_4_deg 12.396 r_dihedral_angle_1_deg 6.562 r_angle_refined_deg 1.461 r_angle_other_deg 1.44 r_chiral_restr 0.077 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.386 r_dihedral_angle_3_deg 14.075 r_dihedral_angle_4_deg 12.396 r_dihedral_angle_1_deg 6.562 r_angle_refined_deg 1.461 r_angle_other_deg 1.44 r_chiral_restr 0.077 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6220 Nucleic Acid Atoms Solvent Atoms 601 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing