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Golgi alpha-mannosidase II D204A catalytic nucleophile mutant with bound mannose.
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. Crystal soaked with
PNP-mannose but only mannose seen in active site, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.607 α = 90 b = 109.508 β = 90 c = 138.607 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 IMAGE PLATE MAR scanner 345 mm plate Osmic mirrors 2002-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.01 20 92 0.068 12.5 3.9 71158 65465
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 2.01 2.08 63.2 0.315 3.4 2 4452
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 2.01 16.52 70253 65361 2318 93.02 0.155 0.154 0.1562 0.174 0.1666 RANDOM 14.051
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] -0.02 -0.03 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.073 r_dihedral_angle_4_deg 17.821 r_dihedral_angle_3_deg 13.312 r_dihedral_angle_1_deg 6.29 r_scangle_it 2.817 r_scbond_it 1.895 r_angle_refined_deg 1.388 r_mcangle_it 1.105 r_mcbond_it 0.741 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.073 r_dihedral_angle_4_deg 17.821 r_dihedral_angle_3_deg 13.312 r_dihedral_angle_1_deg 6.29 r_scangle_it 2.817 r_scbond_it 1.895 r_angle_refined_deg 1.388 r_mcangle_it 1.105 r_mcbond_it 0.741 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.261 r_symmetry_hbond_refined 0.213 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.094 r_metal_ion_refined 0.059 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8193 Nucleic Acid Atoms Solvent Atoms 1034 Heterogen Atoms 35
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection CNS phasing