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Golgi alpha-mannosidase II complex with Noeuromycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HWW PDB Entry 1HWW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 Tris, PEG 6K, MPD, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.16 42.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.502 α = 90 b = 109.19 β = 90 c = 138.148 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 MARRESEARCH Osmic M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 1.86 30 99.2 0.057 29.3 5.6 88093 87388 2 2 13.3
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 1.86 1.9 94.4 0.31 4.55 3.8 5466
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1HWW 1.86 26.85 2 87627 85048 4298 97.1 0.159 0.141 0.141 0.141 0.181 0.1814 RANDOM 19.9
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] -3.87 1.86 2.01
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_scangle_it 4.17 c_scbond_it 2.93 c_mcangle_it 2.36 c_angle_deg 1.8 c_mcbond_it 1.75 c_improper_angle_d 1.2 c_bond_d 0.019 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_scangle_it 4.17 c_scbond_it 2.93 c_mcangle_it 2.36 c_angle_deg 1.8 c_mcbond_it 1.75 c_improper_angle_d 1.2 c_bond_d 0.019 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8181 Nucleic Acid Atoms Solvent Atoms 1073 Heterogen Atoms 34
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing