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BETA-N-ACETYLHEXOSAMINIDASE MUTANT D539A COMPLEXED WITH DI-N-ACETYL-BETA-D-GLUCOSAMINE (CHITOBIASE)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QBB PDB ENTRY 1QBB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 CO-CRYSTALS WERE GROWN BY THE HANGING-DROP VAPOR DIFFUSION METHOD. RESERVOIR BUFFER CONTAINED 2.3 MOLAR AMMONIUM SULFATE AND 100 MILLIMOLAR CACODYLATE BUFFER PH 4.8. PROTEIN SOLUTION 40 MILLIGRAM PER MILLILITER WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR CONTAINING 10 MILLIMOLAR DI-NAG. CRYSTALS ABOUT 0.5 X 0.2 X 0.2 MILLIMETER IN SIZE WERE FORMED WITHIN 2-3 DAYS., VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.56 51.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.794 α = 90 b = 99.96 β = 90 c = 86.308 γ = 90
Symmetry Space Group P 21 21 2
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 345 MM IMAGE PLATE 1999-04-04 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 1.8 15 96.9 0.024 32832 76047
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) 1.8 1.86 90.8 0.095 4738
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 R-FREE PDB ENTRY 1QBB 1.8 15 76047 7659 86.9 0.183 0.171 0.1785 0.224 0.2203 RANDOM 21.8
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 p_staggered_tor 15 p_planar_tor 3.5 p_scangle_it 3.496 p_scbond_it 2.584 p_mcangle_it 2.016 p_mcbond_it 1.481 p_multtor_nbd 0.241 p_singtor_nbd 0.184 p_chiral_restr 0.117 p_planar_d 0.028
RMS Deviations Key Refinement Restraint Deviation p_staggered_tor 15 p_planar_tor 3.5 p_scangle_it 3.496 p_scbond_it 2.584 p_mcangle_it 2.016 p_mcbond_it 1.481 p_multtor_nbd 0.241 p_singtor_nbd 0.184 p_chiral_restr 0.117 p_planar_d 0.028 p_angle_d 0.024 p_bond_d 0.013 p_angle_deg p_hb_or_metal_coord p_plane_restr p_xhyhbond_nbd p_xyhbond_nbd p_orthonormal_tor p_transverse_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6782 Nucleic Acid Atoms Solvent Atoms 823 Heterogen Atoms 49
Software Software Software Name Purpose SCALEPACK data scaling AMoRE phasing REFMAC refinement ARP model building