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Structure of a Paenibacillus polymyxa Xyloglucanase from GH family 44 with Xyloglucan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YKK PDB ENTRY 2YKK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 27% (W/V) PEG 3350, 0.2 M LITHIUM SULPHATE, 0.1 M BIS TRIS PH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.7 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.53 α = 90 b = 83.53 β = 90 c = 157.14 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC CCD 2010-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.7 41.76 95.8 0.09 12 5.3 67177 2 15.3
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 1.7 1.79 93.2 0.42 3.1 4.6
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 2YKK 1.7 41.76 63732 3384 95.2 0.15818 0.15683 0.1558 0.18418 0.1869 RANDOM 14.137
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] 0.58 0.29 0.58 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.151 r_dihedral_angle_4_deg 16.058 r_dihedral_angle_3_deg 11.811 r_dihedral_angle_1_deg 6.507 r_angle_refined_deg 1.341 r_chiral_restr 0.113 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.151 r_dihedral_angle_4_deg 16.058 r_dihedral_angle_3_deg 11.811 r_dihedral_angle_1_deg 6.507 r_angle_refined_deg 1.341 r_chiral_restr 0.113 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3974 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling