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Native family 12 xyloglucanase from Bacillus licheniformis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NLR PDB ENTRY 1NLR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 10% W/V PEG4000, 0.05 M MGCL2, 0.1 M BIS-TRIS, PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.748 α = 90 b = 78.133 β = 109.8 c = 69.103 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE MARRESEARCH MULTILAYER M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.78 20 94.3 0.04 27.7 4.1 44098
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 1.78 1.82 81.5 0.25 4.1 3
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 1NLR 1.78 64.55 42703 1372 94.4 0.156 0.155 0.2 RANDOM 16.21
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] -0.02 -0.07 0.77 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.342 r_dihedral_angle_3_deg 12.012 r_dihedral_angle_4_deg 9.471 r_dihedral_angle_1_deg 7.08 r_scangle_it 2.698 r_scbond_it 1.893 r_angle_refined_deg 1.36 r_mcangle_it 1.196 r_mcbond_it 0.77 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.342 r_dihedral_angle_3_deg 12.012 r_dihedral_angle_4_deg 9.471 r_dihedral_angle_1_deg 7.08 r_scangle_it 2.698 r_scbond_it 1.893 r_angle_refined_deg 1.36 r_mcangle_it 1.196 r_mcbond_it 0.77 r_nbtor_refined 0.304 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.103 r_bond_refined_d 0.013 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 3694 Nucleic Acid Atoms Solvent Atoms 709 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling