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Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35H mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.94 36.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.42 α = 90 b = 86.542 β = 90.02 c = 69.88 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 2008-06-01 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 2 30 97.2 60045 58218 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 1HV1 2 17.47 40275 37754 2021 94.36 0.21324 0.21038 0.213 0.2663 0.2665 RANDOM 9.875
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] -0.05 0.01 -0.01 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.274 r_dihedral_angle_4_deg 16.224 r_dihedral_angle_3_deg 15.199 r_dihedral_angle_1_deg 8.381 r_scangle_it 3.345 r_scbond_it 2.496 r_angle_refined_deg 1.925 r_mcangle_it 1.578 r_mcbond_it 1.005 r_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.274 r_dihedral_angle_4_deg 16.224 r_dihedral_angle_3_deg 15.199 r_dihedral_angle_1_deg 8.381 r_scangle_it 3.345 r_scbond_it 2.496 r_angle_refined_deg 1.925 r_mcangle_it 1.578 r_mcbond_it 1.005 r_chiral_restr 0.138 r_bond_refined_d 0.022 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5800 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 15
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALA data scaling