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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
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 IN A HANGING DROP EXPERIMENT AT 4 DEGREES CENTIGRADE. SUCCESS RATE 1/20
Crystal Properties Matthews coefficient Solvent content 2.43 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.087 α = 90 b = 90.891 β = 90 c = 98.023 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 1.5 20 99.7 0.064 16.21 5 74080 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 1.5 1.53 95.3 0.267 2.57 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 1.5 65.94 70042 3721 99.7 0.145 0.143 0.1571 0.171 0.1804 RANDOM 9.63
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] 0.14 -0.45 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.174 r_dihedral_angle_1_deg 5.688 r_scangle_it 4.27 r_angle_other_deg 3.689 r_scbond_it 2.943 r_angle_refined_deg 2.167 r_mcangle_it 1.972 r_mcbond_it 1.174 r_symmetry_hbond_refined 0.828 r_nbtor_other 0.381
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.174 r_dihedral_angle_1_deg 5.688 r_scangle_it 4.27 r_angle_other_deg 3.689 r_scbond_it 2.943 r_angle_refined_deg 2.167 r_mcangle_it 1.972 r_mcbond_it 1.174 r_symmetry_hbond_refined 0.828 r_nbtor_other 0.381 r_symmetry_vdw_refined 0.275 r_symmetry_vdw_other 0.247 r_nbd_refined 0.239 r_nbd_other 0.199 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.153 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 r_gen_planes_other 0.005 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 3217 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CCP4 phasing