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Golgi alpha-mannosidase II D341N acid-base catalyst 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 in PNP-mannose at 4C, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.67 α = 90 b = 109.486 β = 90 c = 138.584 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 2002-06-15 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 2.03 20 96 0.068 11.6 7.8 69044 66283
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 2.03 2.08 79.8 0.344 4.1 3 3614
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1HTY 2.03 19.79 68416 66227 2347 96.81 0.154 0.152 0.195 0.1567 RANDOM 19.27
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] -0.04 -0.01 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.474 r_dihedral_angle_4_deg 17.174 r_dihedral_angle_3_deg 13.116 r_dihedral_angle_1_deg 6.233 r_scangle_it 2.844 r_scbond_it 1.893 r_angle_refined_deg 1.344 r_mcangle_it 1.134 r_mcbond_it 0.745 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.474 r_dihedral_angle_4_deg 17.174 r_dihedral_angle_3_deg 13.116 r_dihedral_angle_1_deg 6.233 r_scangle_it 2.844 r_scbond_it 1.893 r_angle_refined_deg 1.344 r_mcangle_it 1.134 r_mcbond_it 0.745 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8187 Nucleic Acid Atoms Solvent Atoms 1105 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction PDB_EXTRACT data extraction MAR345dtb data collection CNS phasing