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STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION BY ERWINIA CHRYSANTHEMI GH5 GLUCURONOXYLANASE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NOF PDB ENTRY 1NOF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 CO-CRYSTALLIZATION USING 0.1 M IMIDAZOLE - DL-MALIC ACID BUFFER, PH 7.5 AND 20% PEG 1500 AS PRECIPITANT SOLUTION
Crystal Properties Matthews coefficient Solvent content 2.05 40.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.578 α = 90 b = 59.578 β = 90 c = 168.296 γ = 120
Symmetry Space Group P 32 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 CCD MARRESEARCH SX-165 2009-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.39 20 98.6 0.08 8.5 8.5 70207 1.3 18.9
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 1.39 1.4 98.6 0.42 1.3
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 1NOF 1.39 19.37 66696 3543 98.94 0.12206 0.11956 0.1298 0.1693 0.1727 RANDOM 10.45
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] 0.05 0.03 0.05 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.771 r_dihedral_angle_4_deg 21.946 r_dihedral_angle_3_deg 13.475 r_dihedral_angle_1_deg 6.841 r_scangle_it 5.962 r_scbond_it 4.516 r_mcangle_it 2.974 r_angle_other_deg 2.391 r_mcbond_it 2.168 r_rigid_bond_restr 2.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.771 r_dihedral_angle_4_deg 21.946 r_dihedral_angle_3_deg 13.475 r_dihedral_angle_1_deg 6.841 r_scangle_it 5.962 r_scbond_it 4.516 r_mcangle_it 2.974 r_angle_other_deg 2.391 r_mcbond_it 2.168 r_rigid_bond_restr 2.051 r_angle_refined_deg 1.973 r_mcbond_other 0.951 r_chiral_restr 0.139 r_bond_refined_d 0.024 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2963 Nucleic Acid Atoms Solvent Atoms 571 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling MOLREP phasing