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Crystal structure of family 10 xylanase from Bacillus halodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HIZ PDB ENTRY 1HIZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 30 % (V/V) 2-METHYL-2, 4-PENTANEDIOL, 20 MM CACL2 AND 100 MM SODIUM ACETATE BUFFER (PH 4.6)
Crystal Properties Matthews coefficient Solvent content 2.14 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.602 α = 90 b = 53.586 β = 90 c = 127.565 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH MIRROR 2004-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
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 2.1 65 98.6 0.08 7.9 2.9 21002 2
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 2.1 2.21 98.6 0.31 1.9 2.9
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 1HIZ 2.1 64.55 19843 1067 97.8 0.188 0.185 0.2397 0.241 0.2942 RANDOM 21.52
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] 2.65 -0.66 -1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.341 r_dihedral_angle_4_deg 17.369 r_dihedral_angle_3_deg 16.391 r_dihedral_angle_1_deg 6.214 r_scangle_it 3.403 r_scbond_it 2.171 r_mcangle_it 1.404 r_angle_refined_deg 1.337 r_angle_other_deg 0.923 r_mcbond_it 0.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.341 r_dihedral_angle_4_deg 17.369 r_dihedral_angle_3_deg 16.391 r_dihedral_angle_1_deg 6.214 r_scangle_it 3.403 r_scbond_it 2.171 r_mcangle_it 1.404 r_angle_refined_deg 1.337 r_angle_other_deg 0.923 r_mcbond_it 0.872 r_symmetry_vdw_refined 0.306 r_symmetry_vdw_other 0.279 r_nbd_refined 0.222 r_nbd_other 0.203 r_symmetry_hbond_refined 0.194 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.185 r_nbtor_other 0.089 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 2953 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing