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Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with mannoimidazole
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 1.97 37.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.607 α = 90 b = 143.607 β = 90 c = 50.026 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 CCD ADSC QUANTUM 315r MIRRORS 2012-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.1 46.41 99.2 0.07 18.7 6.2 154906 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 1.1 1.16 94.2 0.28 5.4 4.9
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 1.1 41.49 147134 7772 99.14 0.08932 0.08848 0.1052 0.10524 0.1183 RANDOM 8.403
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.456 r_dihedral_angle_2_deg 33.889 r_dihedral_angle_4_deg 16.49 r_dihedral_angle_3_deg 11.615 r_sphericity_bonded 7.281 r_dihedral_angle_1_deg 6.123 r_rigid_bond_restr 1.614 r_angle_refined_deg 1.392 r_angle_other_deg 0.818 r_symmetry_vdw_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.456 r_dihedral_angle_2_deg 33.889 r_dihedral_angle_4_deg 16.49 r_dihedral_angle_3_deg 11.615 r_sphericity_bonded 7.281 r_dihedral_angle_1_deg 6.123 r_rigid_bond_restr 1.614 r_angle_refined_deg 1.392 r_angle_other_deg 0.818 r_symmetry_vdw_refined 0.306 r_nbd_refined 0.273 r_symmetry_vdw_other 0.266 r_nbtor_refined 0.193 r_nbd_other 0.175 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.106 r_xyhbond_nbd_other 0.1 r_chiral_restr 0.093 r_nbtor_other 0.086 r_metal_ion_refined 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_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 3451 Nucleic Acid Atoms Solvent Atoms 827 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing