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Crystal Structure Of Human Class I alpha-1,2-Mannosidase In Complex With Thio-Disaccharide Substrate Analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FMI PDB ENTRY 1FMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 24% PEG 4000, 50mM ammonium sulfate, 0.1M MES, 10% 1,4-butanediol, pH 6.5, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.93 36.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.687 α = 89.49 b = 53.878 β = 63.6 c = 56.234 γ = 62.61
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 MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.99985 APS 22-ID
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 1.41 50 95.5 0.102 84600
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) 1.41 1.46 93.2 0.129
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 (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 1FMI 1.41 48.8 76092 8507 95.45 0.146 0.14598 0.144 0.1437 0.162 0.1628 RANDOM 8.368
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] 0.26 -0.25 -0.02 -0.07 0.02 0.05
RMS Deviations Key Refinement Restraint Deviation TORSION ANGLES, PERIOD 2 (DEGREES) 32.283 TORSION ANGLES, PERIOD 4 (DEGREES) 13.33 r_dihedral_angle_2_deg 11.599 r_dihedral_angle_1_deg 5.907 r_scangle_it 3.505 r_scbond_it 2.439 r_mcangle_it 2.257 r_mcbond_it 1.717 r_angle_refined_deg 1.337 r_angle_other_deg 0.826
RMS Deviations Key Refinement Restraint Deviation TORSION ANGLES, PERIOD 2 (DEGREES) 32.283 TORSION ANGLES, PERIOD 4 (DEGREES) 13.33 r_dihedral_angle_2_deg 11.599 r_dihedral_angle_1_deg 5.907 r_scangle_it 3.505 r_scbond_it 2.439 r_mcangle_it 2.257 r_mcbond_it 1.717 r_angle_refined_deg 1.337 r_angle_other_deg 0.826 MAIN-CHAIN BOND OTHER ATOMS (A**2) 0.499 r_symmetry_vdw_other 0.24 r_nbd_refined 0.22 NON-BONDED TORSION REFINED ATOMS (A) 0.184 r_nbd_other 0.167 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.095 r_chiral_restr 0.087 r_nbtor_other 0.082 r_symmetry_hbond_refined 0.069 POTENTIAL METAL-ION REFINED ATOMS (A) 0.045 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3668 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 35
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection EPMR phasing