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Crystal Structure of the Family 12 Xyloglucanase from Aspergillus niveus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VL8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.6 291 20% PEG 4000, 0.1M ammonium sulfate, 0.1M sodium acetate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.11 41.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.368 α = 90 b = 62.368 β = 90 c = 226.037 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2001-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.4586 LNLS W01B-MX2
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 2.5 50 96.9 0.108 11.9 4 15884 2 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 2.5 2.59 91.9 0.382 3.1 3.5 1450
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 3VL8 2.5 48.09 2 15864 15063 801 97.14 0.18849 0.18574 0.1942 0.2421 0.245 RANDOM 17.941
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] 0.45 0.45 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.536 r_dihedral_angle_3_deg 15.206 r_dihedral_angle_1_deg 7.594 r_dihedral_angle_4_deg 6.48 r_long_range_B_refined 3.59 r_long_range_B_other 3.587 r_scangle_other 2.558 r_mcangle_it 1.975 r_mcangle_other 1.975 r_angle_refined_deg 1.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.536 r_dihedral_angle_3_deg 15.206 r_dihedral_angle_1_deg 7.594 r_dihedral_angle_4_deg 6.48 r_long_range_B_refined 3.59 r_long_range_B_other 3.587 r_scangle_other 2.558 r_mcangle_it 1.975 r_mcangle_other 1.975 r_angle_refined_deg 1.645 r_scbond_it 1.635 r_scbond_other 1.574 r_mcbond_it 1.182 r_mcbond_other 1.179 r_angle_other_deg 0.79 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3331 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 10
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling