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Structure of the PL6 family alginate lyase Pedsa0632 from Pseudopedobacter saltans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ITG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 0.2 M K sulfate, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.29 α = 90 b = 47.29 β = 98.03 c = 116.73 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 PIXEL DECTRIS EIGER X 4M 2017-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967700 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.99 80.49 94.7 0.998 11.7 6.9 58008
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.04 0.85
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 6ITG 1.99 57.79 57894 2814 94.5 0.2119 0.2102 0.2116 0.2466 0.248 RANDOM 33.19
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] 6.1056 -4.2134 -12.8731 6.7674
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.02 t_omega_torsion 3.79 t_angle_deg 1.07 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.02 t_omega_torsion 3.79 t_angle_deg 1.07 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6270 Nucleic Acid Atoms Solvent Atoms 610 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing