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Golgi alpha-mannosidase II with an empty active site
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 7 293 Tris, NaCl, PEG6000, MPD;
Tris found in the active site under normal
crystallization conditions was removed by
soaking crystals in phosphate buffered
resevoir solution, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.765 α = 90 b = 109.624 β = 90 c = 138.649 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 0.9770 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 1.38 20 98.5 0.06 20.7 6.4 214738 211715 18
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 1.38 1.4 82 0.33 3.5 2.3 3723
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 1.38 19.81 214738 210432 3138 97.99 0.18 0.18 0.1793 0.204 0.184 RANDOM 14.616
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.699 r_dihedral_angle_4_deg 18.041 r_dihedral_angle_3_deg 12.552 r_dihedral_angle_1_deg 6.08 r_scangle_it 3.72 r_scbond_it 2.411 r_mcangle_it 1.68 r_angle_refined_deg 1.544 r_mcbond_it 1.044 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.699 r_dihedral_angle_4_deg 18.041 r_dihedral_angle_3_deg 12.552 r_dihedral_angle_1_deg 6.08 r_scangle_it 3.72 r_scbond_it 2.411 r_mcangle_it 1.68 r_angle_refined_deg 1.544 r_mcbond_it 1.044 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.103 r_metal_ion_refined 0.038 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8196 Nucleic Acid Atoms Solvent Atoms 1470 Heterogen Atoms 39
Software Software Software Name Purpose SAINT data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction SCALEPACK data scaling SADABS data scaling CNS phasing