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vCBM60 in complex with galactobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other APO-VCBM60
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 10MM GALACTOTRIOSE, 0.01M ZINC CHLORIDE, 0.1 M TRIS/HCL PH 8.0, 20% (W/V) PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.71 28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.07 α = 90 b = 49.54 β = 90 c = 54.68 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 CCD ADSC CCD 2009-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.82 36.71 100 0.06 41.5 13.6 7772 2
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 1.82 1.87 100 0.14 15.6 13.5
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 APO-VCBM60 1.82 36.71 7380 355 100 0.14695 0.14471 0.1535 0.19219 0.205 RANDOM 8.943
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] 0.19 -0.49 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.191 r_dihedral_angle_4_deg 16.468 r_dihedral_angle_3_deg 12.516 r_dihedral_angle_1_deg 6.82 r_scangle_it 4.335 r_scbond_it 2.908 r_angle_refined_deg 1.856 r_mcangle_it 1.699 r_angle_other_deg 1.493 r_mcbond_it 1.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.191 r_dihedral_angle_4_deg 16.468 r_dihedral_angle_3_deg 12.516 r_dihedral_angle_1_deg 6.82 r_scangle_it 4.335 r_scbond_it 2.908 r_angle_refined_deg 1.856 r_mcangle_it 1.699 r_angle_other_deg 1.493 r_mcbond_it 1.021 r_mcbond_other 0.369 r_chiral_restr 0.153 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 816 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing