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X-ray crystallographic protein structure of the glycoside hydrolase family 30 subfamily 8 xylanase, Xyn30A, from Clostridium acetobutylicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KL3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294.15 JCSG condition D6: 0.1M HEPES pH 7.5, 4.3 M NaCl
Crystal Properties Matthews coefficient Solvent content 3.11 60.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.483 α = 90 b = 91.866 β = 90 c = 141.251 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 CCD ADSC QUANTUM 315r 2013-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1 SSRL BL7-1
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 1.77 30 100 0.256 6.82 9 51748
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.83 100 1.02 9
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 3KL3 1.77 30 49076 2631 99.8 0.171 0.169 0.1789 0.21 0.2162 RANDOM 16.31
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] -0.55 0.89 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.174 r_dihedral_angle_4_deg 16.373 r_dihedral_angle_3_deg 13.696 r_long_range_B_refined 6.297 r_long_range_B_other 6.297 r_dihedral_angle_1_deg 6.17 r_scangle_other 2.838 r_mcangle_it 1.999 r_mcangle_other 1.999 r_angle_refined_deg 1.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.174 r_dihedral_angle_4_deg 16.373 r_dihedral_angle_3_deg 13.696 r_long_range_B_refined 6.297 r_long_range_B_other 6.297 r_dihedral_angle_1_deg 6.17 r_scangle_other 2.838 r_mcangle_it 1.999 r_mcangle_other 1.999 r_angle_refined_deg 1.938 r_scbond_it 1.925 r_scbond_other 1.914 r_mcbond_it 1.342 r_mcbond_other 1.317 r_angle_other_deg 1.123 r_chiral_restr 0.115 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2972 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing