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Family 5 xyloglucanase from Paenibacillus pabuli in complex with ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JEP PDB ENTRY 2JEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 25% PEG 3350, 0.2 M MGCL2, 0.1 M TRIS, PH 8.5
Crystal Properties Matthews coefficient Solvent content 1.8 32.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.066 α = 90 b = 89.16 β = 90 c = 38.705 γ = 90
Symmetry Space Group P 21 21 2
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 SAGITALLY FOCUSING GE(220) AND A MULTILAYER 2003-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.95 50 98.8 0.11 13.3 4.2 22170
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 1.95 2.02 91.7 0.42 3 4.1
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 2JEP 1.94 61.55 20757 1117 97.9 0.186 0.182 0.1819 0.26 0.2576 RANDOM 21.02
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] -0.25 -1.5 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.077 r_dihedral_angle_4_deg 19.452 r_dihedral_angle_3_deg 14.925 r_dihedral_angle_1_deg 6.182 r_scangle_it 2.861 r_scbond_it 1.947 r_angle_refined_deg 1.443 r_mcangle_it 1.27 r_mcbond_it 0.791 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.077 r_dihedral_angle_4_deg 19.452 r_dihedral_angle_3_deg 14.925 r_dihedral_angle_1_deg 6.182 r_scangle_it 2.861 r_scbond_it 1.947 r_angle_refined_deg 1.443 r_mcangle_it 1.27 r_mcbond_it 0.791 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.203 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 2843 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing