☰ Navigation Tabs
alpha-1,2-mannosidase from Trichoderma reesei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DL2 PDB ENTRY 1DL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 10MG/ML PROTEIN IN 0.1M TRIS-CL PH 7.5 MIX 2 MICROLITER OF PROTEIN SOLUTION WITH 2 MICROLITER OF WELL SOLUTION IN A HANGING DROP EXPERIMENT. THE WELL CONTAINS 0.1M NA-ACETATE PH 4.0, 12% PEG 35000, 0.3M CACL2
Crystal Properties Matthews coefficient Solvent content 2.102 39.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.201 α = 90 b = 106.836 β = 99.42 c = 101.388 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH 2000-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.37 20 98.9 0.083 20.01 4.94 73996 20.4
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 2.37 2.45 95.1 0.214 4.915 4.14
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1DL2 2.37 20 73042 3683 98.8 0.1772 0.1772 0.1808 0.2323 0.2341 RANDOM 21.6
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] -3.94 -5.79 0.71 3.23
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.3 c_scangle_it 2.681 c_mcangle_it 1.956 c_scbond_it 1.796 c_angle_deg 1.5 c_mcbond_it 1.164 c_improper_angle_d 0.86 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.3 c_scangle_it 2.681 c_mcangle_it 1.956 c_scbond_it 1.796 c_angle_deg 1.5 c_mcbond_it 1.164 c_improper_angle_d 0.86 c_bond_d 0.007 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 14846 Nucleic Acid Atoms Solvent Atoms 1094 Heterogen Atoms 144
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing