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High resolution structure of GH11 xylanase from Nectria haematococca
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JRM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293.15 1 M Ammonium sulphate,100mM Sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.446 α = 90 b = 38.5 β = 91.43 c = 53.591 γ = 90
Symmetry Space Group C 1 2 1
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 6M 2018-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97 PETRA III, EMBL c/o DESY P13 (MX1)
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 1 34.67 93.3 0.99 15.5 3.2 82307
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 1 1.06 0.85
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5JRM 1 34.67 77789 4214 92.92 0.1423 0.1417 0.1535 0.1421 RANDOM 9.386
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] 0.03 0.29 -0.43 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.967 r_dihedral_angle_4_deg 16.267 r_dihedral_angle_3_deg 10.386 r_dihedral_angle_1_deg 7.113 r_rigid_bond_restr 2.458 r_angle_refined_deg 1.393 r_angle_other_deg 1.115 r_chiral_restr 0.099 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.967 r_dihedral_angle_4_deg 16.267 r_dihedral_angle_3_deg 10.386 r_dihedral_angle_1_deg 7.113 r_rigid_bond_restr 2.458 r_angle_refined_deg 1.393 r_angle_other_deg 1.115 r_chiral_restr 0.099 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1459 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction