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Golgi mannosidase II D204A catalytic nucleophile mutant with an empty active site
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;
Tris found in the active site under normal
crystallization conditions was removed by
soaking crystals in phosphate buffered
resevoir solution, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.903 α = 90 b = 109.478 β = 90 c = 138.501 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 2003-11-12 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 1.85 30 99.8 0.054 18.8 7.3 90096 89372 28.1
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 1.85 1.89 98.6 0.31 4.3 4.3 5801
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 1.85 19.98 90096 89235 3607 99.04 0.158 0.157 0.1567 0.192 0.1657 RANDOM 18.932
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 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.859 r_dihedral_angle_4_deg 18.458 r_dihedral_angle_3_deg 12.722 r_dihedral_angle_1_deg 6.18 r_scangle_it 2.95 r_scbond_it 1.905 r_angle_refined_deg 1.32 r_mcangle_it 1.224 r_mcbond_it 0.809 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.859 r_dihedral_angle_4_deg 18.458 r_dihedral_angle_3_deg 12.722 r_dihedral_angle_1_deg 6.18 r_scangle_it 2.95 r_scbond_it 1.905 r_angle_refined_deg 1.32 r_mcangle_it 1.224 r_mcbond_it 0.809 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.189 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8194 Nucleic Acid Atoms Solvent Atoms 1498 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction PDB_EXTRACT data extraction MAR345dtb data collection CNS phasing