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Structure of a cold-adapted family 8 xylanase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other WILD TYPE WITHOUT LIGAND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 TAKE 2 - 10 MG/ML PROTEIN IN 20MM MOPS, 50MM NACL, 2% TREHALOSE, PH 7.5. ADD EQUAL VOLUME OF 70% MPD, 0.1M PHOSPHATE BUFFER PH 7.0 WITH 10MG/ML XYLOBIOSE IN A HANGING DROP EXPERIMENT AT 4 DEGREES CENTIGRADE.
Crystal Properties Matthews coefficient Solvent content 2.43 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.972 α = 90 b = 90.734 β = 90 c = 97.581 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
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 1.2 20 99.4 0.032 43.52 5 141707 2
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 1.2 1.22 91.9 0.235 3.69 2.5
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 WILD TYPE WITHOUT LIGAND 1.2 65.94 133682 7056 99.3 0.108 0.107 0.1259 0.13 0.146 RANDOM 10.66
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] -0.22 0.36 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.623 r_dihedral_angle_1_deg 5.866 r_scangle_it 5.613 r_scbond_it 3.882 r_angle_other_deg 3.483 r_mcangle_it 2.441 r_angle_refined_deg 1.816 r_mcbond_it 1.684 r_nbtor_other 0.371 r_symmetry_vdw_refined 0.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.623 r_dihedral_angle_1_deg 5.866 r_scangle_it 5.613 r_scbond_it 3.882 r_angle_other_deg 3.483 r_mcangle_it 2.441 r_angle_refined_deg 1.816 r_mcbond_it 1.684 r_nbtor_other 0.371 r_symmetry_vdw_refined 0.275 r_symmetry_vdw_other 0.265 r_nbd_refined 0.244 r_xyhbond_nbd_refined 0.202 r_nbd_other 0.197 r_chiral_restr 0.196 r_symmetry_hbond_refined 0.194 r_bond_refined_d 0.029 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3203 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CCP4 phasing