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The 3-dimensional structure of a xylanase (Xyn10A) from Cellvibrio japonicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CLX PDB ENTRY 1CLX
Crystallization Crystal Properties Matthews coefficient Solvent content 2.2 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.653 α = 90 b = 95.653 β = 90 c = 150.205 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 120 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.45 25 100 0.05 3.85 8.8 123424
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 1.45 1.5 99.8 0.36 6.76 8
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 1CLX 1.45 24.62 117100 6186 99.9 0.129 0.127 0.1413 0.152 0.1634 RANDOM 11.54
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.486 r_dihedral_angle_4_deg 19.608 r_dihedral_angle_3_deg 11.957 r_dihedral_angle_1_deg 6.445 r_angle_refined_deg 1.402 r_angle_other_deg 0.779 r_nbd_refined 0.259 r_nbd_other 0.238 r_symmetry_vdw_other 0.204 r_symmetry_vdw_refined 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.486 r_dihedral_angle_4_deg 19.608 r_dihedral_angle_3_deg 11.957 r_dihedral_angle_1_deg 6.445 r_angle_refined_deg 1.402 r_angle_other_deg 0.779 r_nbd_refined 0.259 r_nbd_other 0.238 r_symmetry_vdw_other 0.204 r_symmetry_vdw_refined 0.198 r_nbtor_refined 0.194 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.172 r_xyhbond_nbd_other 0.158 r_nbtor_other 0.102 r_chiral_restr 0.091 r_metal_ion_refined 0.036 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 5406 Nucleic Acid Atoms Solvent Atoms 896 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement AMoRE phasing