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A tetragonal-lattice structure of alkaliphilic XynJ from Bacillus sp. 41M-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DCJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 10mM sodium phosphate buffer (Na2HPO4/NaH2PO4), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4 69.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.579 α = 90 b = 116.579 β = 90 c = 45.909 γ = 90
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 RIGAKU JUPITER 210 2005-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1 SPring-8 BL26B1
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 2.1 119.52 99.9 36572 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 100
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 2DCJ 2.1 50 34722 1828 99.62 0.16812 0.16654 0.1808 0.19799 0.1861 RANDOM 27.456
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] 0.55 0.55 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.518 r_scangle_it 4.705 r_scbond_it 3.237 r_mcangle_it 2.285 r_angle_refined_deg 1.985 r_mcbond_it 1.33 r_angle_other_deg 0.944 r_symmetry_vdw_other 0.332 r_symmetry_vdw_refined 0.285 r_nbd_other 0.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.518 r_scangle_it 4.705 r_scbond_it 3.237 r_mcangle_it 2.285 r_angle_refined_deg 1.985 r_mcbond_it 1.33 r_angle_other_deg 0.944 r_symmetry_vdw_other 0.332 r_symmetry_vdw_refined 0.285 r_nbd_other 0.268 r_xyhbond_nbd_refined 0.218 r_nbd_refined 0.196 r_metal_ion_refined 0.17 r_symmetry_hbond_refined 0.168 r_chiral_restr 0.148 r_nbtor_other 0.096 r_bond_refined_d 0.026 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_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 2492 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing