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A bacterial protein structure in glycoside hydrolase family 31.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AED PDB ENTRY 5AED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 25 MG ML-1 YIHQ PROTEIN STOCK IS MIXED WITH EQUAL VOLUME OF PRECIPITANT COMPOSED OF 50-60% (V/V) 2-METHYL-2,4-PENTANEDIOL, 0.1-0.15 M CACL2, AND BIS-TRIS, (PH 6.5) AFTER 3-4 DAYS AT 20 DEGREE. THE LIGAND I5F WAS SOAKED INTO THE NATIVE CRYSTAL.
Crystal Properties Matthews coefficient Solvent content 2 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.665 α = 90 b = 112.643 β = 109.52 c = 111.881 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 293 PIXEL DECTRIS PILATUS 6M 2015-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.85 49.68 98.6 0.05 13.5 4 154198 -3
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 1.85 1.88 95.7 0.62 2.1 3.7
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 5AED 1.85 105.45 146377 7578 98.35 0.16189 0.16026 0.1719 0.19337 0.2002 RANDOM 35.762
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] -1.7 0.91 -2.36 2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.12 r_dihedral_angle_4_deg 17.534 r_dihedral_angle_3_deg 14.556 r_dihedral_angle_1_deg 7.259 r_mcangle_it 4.164 r_scbond_it 3.986 r_mcbond_it 3.231 r_mcbond_other 3.229 r_angle_refined_deg 1.858 r_angle_other_deg 1.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.12 r_dihedral_angle_4_deg 17.534 r_dihedral_angle_3_deg 14.556 r_dihedral_angle_1_deg 7.259 r_mcangle_it 4.164 r_scbond_it 3.986 r_mcbond_it 3.231 r_mcbond_other 3.229 r_angle_refined_deg 1.858 r_angle_other_deg 1.077 r_chiral_restr 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it 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 10757 Nucleic Acid Atoms Solvent Atoms 724 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement MOLREP phasing