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Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant with Glu78 covalently bonded to 2-deoxy-2-fluoro-xylobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.89 34.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.395 α = 90 b = 63.038 β = 104.89 c = 64.36 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 IMAGE PLATE MAR scanner 345 mm plate 2008-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.67 60 98.1 51981 49715 1 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1BVV 1.67 44.28 34541 32247 1722 95.89 0.19083 0.18845 0.1897 0.23562 0.2362 RANDOM 24.222
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] -0.52 -1.33 -0.44 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.329 r_dihedral_angle_4_deg 15.046 r_dihedral_angle_3_deg 12.461 r_dihedral_angle_1_deg 8.778 r_scangle_it 3.799 r_scbond_it 2.883 r_angle_refined_deg 1.929 r_mcangle_it 1.874 r_mcbond_it 1.165 r_chiral_restr 0.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.329 r_dihedral_angle_4_deg 15.046 r_dihedral_angle_3_deg 12.461 r_dihedral_angle_1_deg 8.778 r_scangle_it 3.799 r_scbond_it 2.883 r_angle_refined_deg 1.929 r_mcangle_it 1.874 r_mcbond_it 1.165 r_chiral_restr 0.157 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2898 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 51
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling