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The structure of the family 11 xylanase from Neocallimastix patriciarum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F5J PDB ENTRY 1F5J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M CDCL2, 0.1M SODIUM ACETATE AND 30% V/V PEG400
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.336 α = 90 b = 117.336 β = 90 c = 117.336 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU IMAGE PLATE MIRRORS 2004-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 2.1 37.04 96.8 0.09 7.37 7.49 15357 26
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 2.1 2.21 82.5 0.36 2.07 2.87
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 PDB ENTRY 1F5J 2.1 83.05 15357 766 96.8 0.168 0.166 0.1784 0.205 0.2114 RANDOM 17.2
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.953 r_dihedral_angle_4_deg 26.111 r_dihedral_angle_3_deg 14.314 r_dihedral_angle_1_deg 7.212 r_scangle_it 2.101 r_scbond_it 1.454 r_angle_refined_deg 1.218 r_mcangle_it 0.863 r_mcbond_it 0.789 r_symmetry_vdw_refined 0.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.953 r_dihedral_angle_4_deg 26.111 r_dihedral_angle_3_deg 14.314 r_dihedral_angle_1_deg 7.212 r_scangle_it 2.101 r_scbond_it 1.454 r_angle_refined_deg 1.218 r_mcangle_it 0.863 r_mcbond_it 0.789 r_symmetry_vdw_refined 0.272 r_symmetry_hbond_refined 0.238 r_xyhbond_nbd_refined 0.204 r_nbd_refined 0.183 r_nbtor_refined 0.182 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 1718 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing