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Structure of the GH99 endo-alpha-mannosidase from Bacteriodes thetaiotaomicron in complex with BIS-TRIS-Propane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ACY PDB ENTRY 4ACY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2 M NABR, 20% W/V PEG 3350, 0.1 M BIS-TRIS PROPANE PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.07 40.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.993 α = 90 b = 168.428 β = 117.08 c = 72.433 γ = 90
Symmetry Space Group P 1 21 1
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 CCD MIRRORS 2009-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.1 50 95.3 0.12 7.6 2.8 63710 2 23.2
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 2.1 2.18 97.1 0.46 2.3 2.7
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 4ACY 2.09 48.18 63710 3342 80.72 0.18361 0.18091 0.1583 0.23681 0.2025 RANDOM 25.846
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 -0.77 0.28 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.292 r_dihedral_angle_3_deg 16.315 r_dihedral_angle_4_deg 15.803 r_dihedral_angle_1_deg 6.247 r_angle_refined_deg 1.376 r_mcangle_it 1.376 r_nbtor_refined 0.316 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.292 r_dihedral_angle_3_deg 16.315 r_dihedral_angle_4_deg 15.803 r_dihedral_angle_1_deg 6.247 r_angle_refined_deg 1.376 r_mcangle_it 1.376 r_nbtor_refined 0.316 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.155 r_chiral_restr 0.096 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 10346 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing