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Polysaccharide Lyase BACCELL_00875
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CE7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 200 mM sodium malonate
20% polyethylene glycol (PEG) 3350.
Crystal Properties Matthews coefficient Solvent content 1.86 33.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.398 α = 90 b = 88.398 β = 90 c = 215.857 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9798 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.26 21.13 99.5 0.998 13 8.8 87238
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.26 1.28 94.3 0.524 3.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4CE7 1.26 21.13 81513 4229 97.74 0.12268 0.12135 0.14801 0.1694 RANDOM 12.271
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] 0.09 0.05 0.09 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.737 r_dihedral_angle_4_deg 18.841 r_sphericity_free 18.443 r_dihedral_angle_3_deg 11.535 r_sphericity_bonded 6.215 r_dihedral_angle_1_deg 5.743 r_long_range_B_refined 2.454 r_long_range_B_other 2.349 r_scangle_other 2.238 r_rigid_bond_restr 1.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.737 r_dihedral_angle_4_deg 18.841 r_sphericity_free 18.443 r_dihedral_angle_3_deg 11.535 r_sphericity_bonded 6.215 r_dihedral_angle_1_deg 5.743 r_long_range_B_refined 2.454 r_long_range_B_other 2.349 r_scangle_other 2.238 r_rigid_bond_restr 1.954 r_scbond_it 1.864 r_scbond_other 1.863 r_mcangle_other 1.539 r_mcangle_it 1.535 r_angle_refined_deg 1.517 r_mcbond_it 1.166 r_mcbond_other 1.149 r_angle_other_deg 0.994 r_chiral_restr 0.113 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2893 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms
Software Software Software Name Purpose iMOSFLM data reduction Aimless data scaling MrBUMP phasing PHASER phasing BUCCANEER model building ARP model building WARP model building REFMAC refinement