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Multi-domain GH92 alpha-1,2-mannosidase from Neobacillus novalis: mannoimidazole complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WZS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 21% PEG 3350, 0.1 M bis-Tris-propane pH 6.6, 0.2M sodium citrate, MMS
Crystal Properties Matthews coefficient Solvent content 2.63 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.605 α = 90 b = 151.937 β = 94.63 c = 114.007 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 PIXEL DECTRIS PILATUS 6M-F 2018-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.29 47.923 98.1 0.132 0.186 0.131 0.981 5.1 2.9 141182
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.33 99.5 0.777 1.09 0.763 0.505 1.1 3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2wzs 2.29 47.923 141144 6947 97.987 0.207 0.2053 0.2053 0.2458 0.2459 32.923
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] 1.719 -4.093 -0.854 -0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.222 r_dihedral_angle_4_deg 17.692 r_dihedral_angle_3_deg 16.452 r_lrange_it 9.701 r_dihedral_angle_1_deg 7.254 r_scangle_it 5.139 r_mcangle_it 4.344 r_scbond_it 3.548 r_mcbond_it 2.927 r_angle_refined_deg 1.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.222 r_dihedral_angle_4_deg 17.692 r_dihedral_angle_3_deg 16.452 r_lrange_it 9.701 r_dihedral_angle_1_deg 7.254 r_scangle_it 5.139 r_mcangle_it 4.344 r_scbond_it 3.548 r_mcbond_it 2.927 r_angle_refined_deg 1.533 r_nbtor_refined 0.312 r_nbd_refined 0.216 r_symmetry_xyhbond_nbd_refined 0.203 r_symmetry_nbd_refined 0.161 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.113 r_ncsr_local_group_1 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20140 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms 89
Software Software Software Name Purpose XDS data reduction XDS data scaling xia2 data reduction xia2 data scaling Aimless data scaling MOLREP phasing REFMAC refinement