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Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other PREVIOUSLY SOLVED STRUCTURE OF CLOSELY RELATED HOMOLOG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.1 M SODIUM ACETATE PH 4.9, 20% W/V PEG 2000 MME, 1.6% PGA-LM (POLY-GAMMA-GLUTAMIC ACID LOW MOLECULAR WEIGHT)
Crystal Properties Matthews coefficient Solvent content 2.32 47.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.54 α = 90 b = 108.54 β = 90 c = 67.75 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 IMAGE PLATE MARRESEARCH OSMICS MULTILAYER OPTICS 2011-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.9 40 100 0.046 24.2 5 31100 2 14.3
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 1.9 2 100 0.15 8.8 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 STRUCTURE OF CLOSELY RELATED HOMOLOG 1.9 38.37 29524 1569 99.96 0.15132 0.14951 0.1495 0.18549 0.185 RANDOM 14.696
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_dihedral_angle_2_deg 37.571 r_dihedral_angle_4_deg 13.71 r_dihedral_angle_3_deg 13.377 r_dihedral_angle_1_deg 5.967 r_angle_refined_deg 1.205 r_mcangle_it 1.205 r_nbtor_refined 0.312 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.178 r_symmetry_hbond_refined 0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.571 r_dihedral_angle_4_deg 13.71 r_dihedral_angle_3_deg 13.377 r_dihedral_angle_1_deg 5.967 r_angle_refined_deg 1.205 r_mcangle_it 1.205 r_nbtor_refined 0.312 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.178 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_mcbond_it 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2823 Nucleic Acid Atoms Solvent Atoms 467 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing