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Structural and active site modification studies implicate Glu, Trp and Arg in the activity of xylanase from alkalophilic Bacillus sp. (NCL 87-6-10).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H4G PDB ENTRY 1H4G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 Isopropanal 30%,Sodium citrate 0.2M, Sodium Cacodylate buffer(0.1M) of pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.45 49.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.421 α = 90 b = 77.281 β = 90 c = 79.233 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 295 IMAGE PLATE RIGAKU RAXIS IV Osmic mirrors 2004-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.8 55 93.9 0.071 12.64 4.127 11622 11586 1 1 48.349
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) 2.8 2.9 93.9 0.071 12.64 4.127 10868
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1H4G 2.8 55.05 1 1 10334 519 93.72 0.17102 0.16917 0.16632 0.1628 0.22649 0.219 RANDOM 35.209
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] -0.2 4.27 -4.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.731 r_scangle_it 3.352 r_scbond_it 1.958 r_angle_refined_deg 1.71 r_mcangle_it 1.575 r_mcbond_it 0.918 r_symmetry_vdw_refined 0.288 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.731 r_scangle_it 3.352 r_scbond_it 1.958 r_angle_refined_deg 1.71 r_mcangle_it 1.575 r_mcbond_it 0.918 r_symmetry_vdw_refined 0.288 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.112 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3238 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing