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Crystal structure of Nostoc Punctiforme Debranching Enzyme(NPDE)(Acarbose soaked)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J0H PDB ENTRY 1J0H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 20%(W/V)PEG 8000,0.2M TRIC-CL, 0.1M MGCL2, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.58 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.968 α = 90 b = 86.968 β = 90 c = 262.393 γ = 120
Symmetry Space Group P 61 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 95 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A PAL/PLS 4A
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 2.37 30 99 0.09 10.8 12.8 24597 15.5
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 2.37 2.45 98.8 0.27 5.09 8.7
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 THROUGHOUT PDB ENTRY 1J0H 2.37 28.54 24597 1190 99 0.215 0.215 0.2099 0.269 0.2632 RANDOM 27.8
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] 4.28 4.28 -8.56
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.3 c_angle_deg 1.2 c_improper_angle_d 0.83 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.3 c_angle_deg 1.2 c_improper_angle_d 0.83 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3790 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PHASER phasing