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Structure of a Paenibacillus Polymyxa Xyloglucanase from Glycoside Hydrolase Family 44
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 25% (W/V) PEG 3350, 0.2M LITHIUM SULPHATE, 0.1M HEPES PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.61 α = 90 b = 83.61 β = 90 c = 157.531 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 IMAGE PLATE MARRESEARCH OSMIC M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.86 42.52 99.5 0.06 26.3 7 54053 2 13.8
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 1.86 1.96 96.6 0.13 11.3 6.5
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 1.86 22.23 51240 2720 99.41 0.13837 0.13669 0.1357 0.17122 0.1713 RANDOM 13.456
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] 0.33 0.16 0.33 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.717 r_dihedral_angle_4_deg 16.534 r_dihedral_angle_3_deg 12.604 r_dihedral_angle_1_deg 6.142 r_angle_refined_deg 1.553 r_chiral_restr 0.122 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.717 r_dihedral_angle_4_deg 16.534 r_dihedral_angle_3_deg 12.604 r_dihedral_angle_1_deg 6.142 r_angle_refined_deg 1.553 r_chiral_restr 0.122 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 3992 Nucleic Acid Atoms Solvent Atoms 688 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling