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Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with noeuromycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AYQ PDB ENTRY 4AYQ
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 1.99 38.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.919 α = 90 b = 143.919 β = 90 c = 50.186 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 2M MIRRORS 2012-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 46.55 89.6 0.04 32.2 9.1 140945 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 49.5 0.21 6.7 4.2
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 4AYQ 1.1 46.6 133840 7105 89.53 0.08362 0.08264 0.1024 0.10208 0.1159 RANDOM 9.843
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_sphericity_free 36.735 r_dihedral_angle_2_deg 33.099 r_dihedral_angle_4_deg 16.668 r_dihedral_angle_3_deg 12.157 r_sphericity_bonded 7.229 r_dihedral_angle_1_deg 6.001 r_rigid_bond_restr 1.588 r_angle_refined_deg 1.394 r_angle_other_deg 0.816 r_symmetry_vdw_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.735 r_dihedral_angle_2_deg 33.099 r_dihedral_angle_4_deg 16.668 r_dihedral_angle_3_deg 12.157 r_sphericity_bonded 7.229 r_dihedral_angle_1_deg 6.001 r_rigid_bond_restr 1.588 r_angle_refined_deg 1.394 r_angle_other_deg 0.816 r_symmetry_vdw_refined 0.338 r_symmetry_hbond_refined 0.338 r_chiral_restr 0.28 r_nbd_refined 0.275 r_symmetry_vdw_other 0.274 r_nbtor_refined 0.188 r_nbd_other 0.172 r_xyhbond_nbd_refined 0.171 r_nbtor_other 0.085 r_metal_ion_refined 0.054 r_xyhbond_nbd_other 0.019 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 3429 Nucleic Acid Atoms Solvent Atoms 724 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing