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A two-domain structure of alkaliphilic XynJ from Bacillus sp. 41M-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 296 0.1M Hepes buffer pH 8.0, 0.35M Sodium citrate, 10% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 4.64 73.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.927 α = 90 b = 122.927 β = 90 c = 331.943 γ = 120
Symmetry Space Group P 61 2 2
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 2002-06-16 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 2.24 49.39 100 72194 -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 2.24 2.32 100
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1QH7 2.24 49.39 68253 3634 99.85 0.16048 0.15883 0.19116 0.1794 RANDOM 29.252
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.679 r_scangle_it 4.397 r_scbond_it 3.003 r_angle_refined_deg 2.013 r_mcangle_it 1.906 r_mcbond_it 1.103 r_angle_other_deg 0.984 r_symmetry_hbond_refined 0.273 r_nbd_other 0.272 r_symmetry_vdw_other 0.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.679 r_scangle_it 4.397 r_scbond_it 3.003 r_angle_refined_deg 2.013 r_mcangle_it 1.906 r_mcbond_it 1.103 r_angle_other_deg 0.984 r_symmetry_hbond_refined 0.273 r_nbd_other 0.272 r_symmetry_vdw_other 0.243 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.207 r_chiral_restr 0.151 r_metal_ion_refined 0.115 r_symmetry_vdw_refined 0.103 r_nbtor_other 0.094 r_bond_refined_d 0.025 r_gen_planes_other 0.019 r_gen_planes_refined 0.016 r_bond_other_d 0.003 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 5055 Nucleic Acid Atoms Solvent Atoms 879 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing