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Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with thiomannobioside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other PREVIOUSLY SOLVED NATIVE STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2 M AMMONIUM ACTETATE, 0.1 M BIS-TRIS PH 6.5, 22% WT/VOL PEG 3350
Crystal Properties Matthews coefficient Solvent content 2 38.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.135 α = 90 b = 144.135 β = 90 c = 50.301 γ = 120
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 MIRRORS 2011-07-11 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 0.85 46.65 97.2 0.04 16.9 5.1 333281 1.7
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 0.85 0.9 80.8 0.57 1.7 2.8
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 PREVIOUSLY SOLVED NATIVE STRUCTURE 0.85 39.16 316449 16821 97.17 0.09692 0.09646 0.1073 0.10555 0.1161 RANDOM 8.802
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] 0.04 0.02 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.618 r_dihedral_angle_2_deg 34.332 r_dihedral_angle_4_deg 17.833 r_dihedral_angle_3_deg 11.963 r_sphericity_bonded 9.068 r_dihedral_angle_1_deg 6.041 r_rigid_bond_restr 2.031 r_angle_refined_deg 1.427 r_angle_other_deg 0.801 r_symmetry_hbond_refined 0.616
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 35.618 r_dihedral_angle_2_deg 34.332 r_dihedral_angle_4_deg 17.833 r_dihedral_angle_3_deg 11.963 r_sphericity_bonded 9.068 r_dihedral_angle_1_deg 6.041 r_rigid_bond_restr 2.031 r_angle_refined_deg 1.427 r_angle_other_deg 0.801 r_symmetry_hbond_refined 0.616 r_symmetry_vdw_refined 0.321 r_nbd_refined 0.282 r_symmetry_vdw_other 0.235 r_nbtor_refined 0.186 r_symmetry_hbond_other 0.183 r_nbd_other 0.168 r_xyhbond_nbd_refined 0.114 r_nbtor_other 0.085 r_chiral_restr 0.082 r_metal_ion_refined 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3449 Nucleic Acid Atoms Solvent Atoms 781 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing