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Native Bacillus subtilis Arabinanase Arb43A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GYD PDB ENTRY 1GYD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.2M MGCL2, 15% PEG 3350 5MM CACL2, 10 MM TRIS PH 8.0, 25% ETHYLENE GLYCOL
Crystal Properties Matthews coefficient Solvent content 2.1 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.628 α = 90 b = 46.153 β = 98.96 c = 57.322 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 CCD ADSC CCD MIRROR 2002-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 SRS PX14.1
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 1.5 28.3 91 0.071 18.2 4 40400
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 1.5 1.58 74.5 0.208 4.3 3
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1GYD 1.5 20 34795 1840 90.8 0.169 0.167 0.1824 0.199 RANDOM 13.27
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] 0.6 0.08 -0.13 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.341 r_scangle_it 3.267 r_scbond_it 2.246 r_angle_refined_deg 1.668 r_mcangle_it 1.401 r_angle_other_deg 1.388 r_mcbond_it 0.86 r_xyhbond_nbd_refined 0.347 r_symmetry_vdw_other 0.287 r_nbd_other 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.341 r_scangle_it 3.267 r_scbond_it 2.246 r_angle_refined_deg 1.668 r_mcangle_it 1.401 r_angle_other_deg 1.388 r_mcbond_it 0.86 r_xyhbond_nbd_refined 0.347 r_symmetry_vdw_other 0.287 r_nbd_other 0.26 r_symmetry_hbond_refined 0.204 r_nbd_refined 0.202 r_chiral_restr 0.139 r_symmetry_vdw_refined 0.109 r_metal_ion_refined 0.101 r_nbtor_other 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 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_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 2263 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing