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Golgi mannosidase II D204A catalytic nucleophile mutant complex with Tris
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 is found in the active site under
normal crystallization conditions, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.259 α = 90 b = 108.988 β = 90 c = 137.569 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 CCD ADSC QUANTUM 4 2005-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.912 CHESS F1
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 1.25 30 93.1 0.079 13.2 6.9 282754 263244 15.1
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) 1.25 1.28 56.3 0.316 4.7 3.7 10488
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB entry 1HTY 1.25 10 258473 252996 3916 91.8 0.125 0.121 0.1151 0.159 RANDOM 16.7
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]
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.089 s_non_zero_chiral_vol 0.083 s_zero_chiral_vol 0.076 s_similar_adp_cmpnt 0.046 s_angle_d 0.032 s_from_restr_planes 0.03 s_anti_bump_dis_restr 0.027 s_bond_d 0.012 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8543 Nucleic Acid Atoms Solvent Atoms 1537 Heterogen Atoms 10
Software Software Software Name Purpose SHELXL-97 refinement SCALEPACK data scaling CNS refinement SHELX refinement PDB_EXTRACT data extraction ADSC data collection CNS phasing DENZO data reduction