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crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus in complex with Pentaerythritol propoxylate (5 4 PO OH)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G3M PDB ENTRY 2G3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 40 % PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), 0.1 M BIS-TRIS (PH 7.0), 5 MM NI SO4
Crystal Properties Matthews coefficient Solvent content 3.53 65.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.653 α = 90 b = 157.653 β = 90 c = 226.688 γ = 120
Symmetry Space Group P 63 2 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 CCD ADSC QUANTUM 315r MIRRORS 2009-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.3 58.5 100 0.17 16.3 11.3 74143 -3 24.33
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 2.3 2.42 100 0.47 7.5 4.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2G3M 2.3 54.548 1.38 74143 3736 99.99 0.147 0.145 0.1445 0.1853 0.1838
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] 2.8439 2.8439 -5.6878
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.183 f_angle_d 1.043 f_chiral_restr 0.07 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7572 Nucleic Acid Atoms Solvent Atoms 714 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling BALBES phasing