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Crystal structure of the Nasturtium seedling xyloglucanase isoform NXG1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UN1 PDB ENTRY 1UN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 THE SOLUTIONS FOR THE OPTIMIZED CONDITIONS OF NXG1 CONTAINED 15-20% OF POLYETHYLENE GLYCOL (PEG) 20000 AND 100 MM HEPES BUFFER AT PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.64 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.109 α = 90 b = 116.109 β = 90 c = 63.071 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 CCD ADSC CCD 2006-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.8 45 99.4 0.12 9.8 4.5 87640 0.5
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 1.8 1.9 98.9 0.65 2.4 4.4
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1UN1 1.8 40.5 83243 4392 99.4 0.177 0.176 0.2 RANDOM 14.57
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] 0.14 0.07 0.14 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.722 r_dihedral_angle_4_deg 13.897 r_dihedral_angle_3_deg 13.194 r_dihedral_angle_1_deg 6.788 r_scangle_it 1.932 r_scbond_it 1.326 r_angle_refined_deg 1.25 r_angle_other_deg 0.768 r_mcangle_it 0.748 r_mcbond_it 0.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.722 r_dihedral_angle_4_deg 13.897 r_dihedral_angle_3_deg 13.194 r_dihedral_angle_1_deg 6.788 r_scangle_it 1.932 r_scbond_it 1.326 r_angle_refined_deg 1.25 r_angle_other_deg 0.768 r_mcangle_it 0.748 r_mcbond_it 0.649 r_nbd_refined 0.202 r_nbtor_refined 0.189 r_nbd_other 0.186 r_symmetry_hbond_refined 0.186 r_symmetry_vdw_other 0.183 r_xyhbond_nbd_refined 0.14 r_symmetry_vdw_refined 0.105 r_nbtor_other 0.082 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 6639 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing