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Crystal structure of GH30_8 xylanase from Bacillus pumilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GTN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 20% (w/v) PEG 3350 and 0.18 M ammonium citrate
Crystal Properties Matthews coefficient Solvent content 2.7 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.084 α = 90 b = 101.484 β = 90 c = 158.689 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 2M 2022-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.977 LNLS SIRIUS MANACA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.16 48.65 98.54 0.996 8.58 2 51299 35.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.16 2.237 0.489
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.16 48.65 48736 2567 98.5 0.1934 0.19224 0.2004 0.21547 0.2273 RANDOM 39.817
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] -0.23 -1 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.688 r_long_range_B_refined 5.939 r_long_range_B_other 5.913 r_dihedral_angle_1_deg 5.744 r_scangle_other 4.627 r_mcangle_it 3.226 r_mcangle_other 3.226 r_scbond_it 2.952 r_scbond_other 2.952 r_mcbond_it 2.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.688 r_long_range_B_refined 5.939 r_long_range_B_other 5.913 r_dihedral_angle_1_deg 5.744 r_scangle_other 4.627 r_mcangle_it 3.226 r_mcangle_other 3.226 r_scbond_it 2.952 r_scbond_other 2.952 r_mcbond_it 2.129 r_mcbond_other 2.129 r_angle_refined_deg 0.837 r_angle_other_deg 0.322 r_chiral_restr 0.044 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6230 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction XSCALE data scaling PHASER phasing