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Crystal Structure of Debranching enzyme from Nostoc punctiforme (NPDE)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WC7 PDB ENTRY 2WC7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 20%(W/V)POLYETHYLENE GYLCOL, 200MM TRIC-CL (PH8.5),100MM MGCL2
Crystal Properties Matthews coefficient Solvent content 2.93 58.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.731 α = 90 b = 93.731 β = 90 c = 257.042 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 2.8 30 100 0.09 11.3 22.8 16274 86.7
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 2.8 2.85 100 0.56 7.2 23.9
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 2WC7 2.8 29.88 16274 785 94.2 0.224 0.224 0.221 0.284 0.2805 RANDOM 54.9
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] 12.02 12.02 -24.04
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_improper_angle_d 2.5 c_angle_deg 1.1 c_bond_d 0.005 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 25 c_improper_angle_d 2.5 c_angle_deg 1.1 c_bond_d 0.005 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 3922 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PHASER phasing