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crystal structure of Dpo31, of a tail-spike protein with depolymerase activity identified in a marine podovirus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 Hanging drops, 2 microL of protein (12 mg/ml) with 1 microL of reservoir solution
1.2 M Ammonium sulfate and 100 mM Citric acid at pH 5.0
Crystal Properties Matthews coefficient Solvent content 3.53 65.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.2 α = 90 b = 88.2 β = 90 c = 643.33 γ = 120
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 4 2019-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97911 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.2 49.2 43.7 0.115 0.026 1 18.4 21.2 22469 46.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 5.7 0.875 0.295 0.787 8.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.2 49.2 22468 1092 43.2 0.253 0.252 0.2412 0.273 0.2582 RANDOM 57.35
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] -0.3265 -0.3265 0.6531
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.99 t_omega_torsion 2.7 t_angle_deg 0.83 t_bond_d 0.005 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.99 t_omega_torsion 2.7 t_angle_deg 0.83 t_bond_d 0.005 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 4789 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 40
Software Software Software Name Purpose BUSTER refinement Aimless data scaling XDS data reduction PHASER phasing PHASER phasing PDB_EXTRACT data extraction