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Catalytic domain of Coprinopsis cinerea GH62 alpha-L-arabinofuranosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 MES buffer, NaBr, PEG 20000
Crystal Properties Matthews coefficient Solvent content 1.88 34.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.713 α = 90 b = 77.735 β = 93 c = 74.202 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 210r 2014-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.7 74.1 99.4 0.108 15.1 3.7 59017
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 1.7 1.76 97.2 0.545 2.7 3.5
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 5B6T 1.7 74.1 56138 2852 99.2 0.14062 0.1391 0.154 0.17017 0.1816 RANDOM 14.261
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 29.152 r_dihedral_angle_4_deg 17.982 r_dihedral_angle_3_deg 11.686 r_dihedral_angle_1_deg 7.458 r_long_range_B_refined 4.335 r_long_range_B_other 3.838 r_angle_other_deg 3.729 r_scangle_other 1.821 r_angle_refined_deg 1.376 r_mcangle_it 1.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.152 r_dihedral_angle_4_deg 17.982 r_dihedral_angle_3_deg 11.686 r_dihedral_angle_1_deg 7.458 r_long_range_B_refined 4.335 r_long_range_B_other 3.838 r_angle_other_deg 3.729 r_scangle_other 1.821 r_angle_refined_deg 1.376 r_mcangle_it 1.258 r_mcangle_other 1.258 r_scbond_it 1.156 r_scbond_other 1.156 r_mcbond_it 0.762 r_mcbond_other 0.762 r_chiral_restr 0.085 r_gen_planes_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5014 Nucleic Acid Atoms Solvent Atoms 675 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing