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Golgi mannosidase II complex with MANNOSTATIN B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HTY PDB entry 1HTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 PEG8000, Tris, 2.5% MPD, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.63 α = 90 b = 109.281 β = 90 c = 137.77 γ = 90
Symmetry Space Group P 21 21 21
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 4 2007-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.977 CHESS A1
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 1.4 25 96.3 0.05 17.3 4.9 203583 196104
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) 1.4 1.45 73.8 0.29 3.8 2.3 16295
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1HTY 1.4 24.9 203600 193351 2892 95.05 0.142 0.142 0.1447 0.164 0.1473 RANDOM 18.073
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 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.621 r_dihedral_angle_4_deg 18.298 r_dihedral_angle_3_deg 12.848 r_dihedral_angle_1_deg 6.123 r_sphericity_free 5.387 r_scangle_it 4.022 r_sphericity_bonded 3.786 r_scbond_it 2.948 r_rigid_bond_restr 2.061 r_mcangle_it 2.037
Show All KeysRMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.621 r_dihedral_angle_4_deg 18.298 r_dihedral_angle_3_deg 12.848 r_dihedral_angle_1_deg 6.123 r_sphericity_free 5.387 r_scangle_it 4.022 r_sphericity_bonded 3.786 r_scbond_it 2.948 r_rigid_bond_restr 2.061 r_mcangle_it 2.037 r_angle_refined_deg 1.465 r_mcbond_it 1.38 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.149 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.008
Hide All KeysNon-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8348 Nucleic Acid Atoms Solvent Atoms 1178 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement CNS refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SADABS data scaling CNS phasing