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Structure of Xyn11 from Pseudothermotoga thermarum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 10% PEG 3350, 0.2 M Proline, 0.1 M Hepes pH 7.5. Mother liquor solution was supplemented by 25% of glycerol to cryoprotect the crystal during the data collection.
Crystal Properties Matthews coefficient Solvent content 2.76 53.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.452 α = 90 b = 95.268 β = 90 c = 100.527 γ = 90
Symmetry Space Group P 21 21 21
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 2020-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979257 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 1.8 47.63 99.9 0.09 0.098 0.038 0.998 13 6.5 81903
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 1.8 1.83 100 0.684 0.745 0.293 0.882 2.7 6.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5OFJ 1.8 44.5 77764 4055 99.89 0.1576 0.1561 0.1841 0.1874 RANDOM 26.006
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] 2.12 -0.97 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.161 r_dihedral_angle_4_deg 14.989 r_dihedral_angle_3_deg 12.895 r_dihedral_angle_1_deg 6.829 r_angle_refined_deg 1.435 r_angle_other_deg 1.414 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.161 r_dihedral_angle_4_deg 14.989 r_dihedral_angle_3_deg 12.895 r_dihedral_angle_1_deg 6.829 r_angle_refined_deg 1.435 r_angle_other_deg 1.414 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5604 Nucleic Acid Atoms Solvent Atoms 716 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing