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Native family 5 xyloglucanase from Paenibacillus pabuli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ECG PDB ENTRY 1ECG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 20-25% PEG 8000, 0.2 M CACL2, 0.1 M TRIS, PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.1 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.416 α = 90 b = 89.574 β = 90 c = 90.397 γ = 90
Symmetry Space Group P 21 21 21
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 CCD TOROIDAL MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.4 30 99.7 0.04 42.2 4.4 134851
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 1.4 1.42 98.6 0.11 9.1 3.2
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 PDB ENTRY 1ECG 1.4 63.25 128009 6771 99.6 0.116 0.115 0.144 0.1668 RANDOM 8.77
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] 0.66 -0.09 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.346 r_dihedral_angle_4_deg 15.08 r_dihedral_angle_3_deg 10.485 r_dihedral_angle_1_deg 5.876 r_scangle_it 3.276 r_scbond_it 2.508 r_mcangle_it 1.748 r_angle_refined_deg 1.419 r_mcbond_it 1.248 r_angle_other_deg 0.963
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.346 r_dihedral_angle_4_deg 15.08 r_dihedral_angle_3_deg 10.485 r_dihedral_angle_1_deg 5.876 r_scangle_it 3.276 r_scbond_it 2.508 r_mcangle_it 1.748 r_angle_refined_deg 1.419 r_mcbond_it 1.248 r_angle_other_deg 0.963 r_nbd_refined 0.223 r_symmetry_vdw_other 0.218 r_nbd_other 0.193 r_nbtor_refined 0.19 r_symmetry_hbond_refined 0.164 r_symmetry_vdw_refined 0.149 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.092 r_nbtor_other 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 5729 Nucleic Acid Atoms Solvent Atoms 1278 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing