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Crystal structure of endo-arabinanase ABN-TS D147N mutant in complex with arabinohexaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WL7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 16% PEG 8000, 0.2M magnesium chloride, 0.1M MES pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.27 45.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.809 α = 90 b = 92.26 β = 91.52 c = 78.673 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 100 CCD ADSC QUANTUM 4 2008-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.978 Photon Factory BL-6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.9 50 99.2 0.055 13.9 3.7 51538 15.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 97.6 0.324 3.6
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 1WL7 1.9 50 48588 2625 99.28 0.18358 0.18092 0.23286 0.2222 RANDOM 23.416
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.021 r_dihedral_angle_3_deg 14.3 r_dihedral_angle_4_deg 13.432 r_dihedral_angle_1_deg 7.578 r_long_range_B_refined 6.377 r_long_range_B_other 6.199 r_scangle_other 4.501 r_scbond_other 2.959 r_scbond_it 2.958 r_mcangle_it 2.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.021 r_dihedral_angle_3_deg 14.3 r_dihedral_angle_4_deg 13.432 r_dihedral_angle_1_deg 7.578 r_long_range_B_refined 6.377 r_long_range_B_other 6.199 r_scangle_other 4.501 r_scbond_other 2.959 r_scbond_it 2.958 r_mcangle_it 2.836 r_mcangle_other 2.836 r_angle_refined_deg 1.977 r_mcbond_it 1.916 r_mcbond_other 1.916 r_angle_other_deg 1.049 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5112 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing