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Crystal structure of the catalytic domain of beta-agarase D from Zobellia galactanivorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O4Z PDB ENTRY 1O4Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 28-34 % PEG 8000 AND 0,1 M IMIDAZOLE PH 8, 4% ISOPROPANOL
Crystal Properties Matthews coefficient Solvent content 2.14 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.247 α = 90 b = 77.268 β = 90 c = 83.695 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 100 CCD ADSC QUANTUM 210 2008-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 56 99.9 0.05 21.3 6.9 55977 0.1
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 99.9 0.25 9.1 6.9
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 1O4Z 1.5 56.8 53071 2839 99.85 0.16354 0.16215 0.1619 0.18987 0.1901 RANDOM 13.7
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] 0.06 -0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.495 r_dihedral_angle_4_deg 18.631 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 6.981 r_scangle_it 2.82 r_scbond_it 1.958 r_angle_refined_deg 1.441 r_mcangle_it 1.283 r_angle_other_deg 0.876 r_mcbond_it 0.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.495 r_dihedral_angle_4_deg 18.631 r_dihedral_angle_3_deg 12.873 r_dihedral_angle_1_deg 6.981 r_scangle_it 2.82 r_scbond_it 1.958 r_angle_refined_deg 1.441 r_mcangle_it 1.283 r_angle_other_deg 0.876 r_mcbond_it 0.784 r_nbd_other 0.324 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.2 r_symmetry_hbond_refined 0.179 r_chiral_restr 0.127 r_metal_ion_refined 0.075 r_nbtor_other 0.048 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other r_xyhbond_nbd_other 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_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 2843 Nucleic Acid Atoms Solvent Atoms 595 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing