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Peptide Asparaginyl Ligases from Viola yedoensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293 PEG 3350, 0.2m Magnesium formate
Crystal Properties Matthews coefficient Solvent content 2.53 56.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.8 α = 90 b = 69.8 β = 110.22 c = 104.48 γ = 90
Symmetry Space Group C 1 2 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 16M 2018-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953723 Australian Synchrotron MX2
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 2.4 50 99.4 0.21 5.78 3.8 41522 56.75
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 2.4 2.54 1.24
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 5H0I 2.4 48 41522 2077 99.6 0.219 0.195 0.1996 0.2363 0.2414 RANDOM 47.02
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] -1.1313 7.0276 5.082 -3.9506
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.01 t_omega_torsion 2.77 t_angle_deg 1.16 t_bond_d 0.01 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 21.01 t_omega_torsion 2.77 t_angle_deg 1.16 t_bond_d 0.01 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 6578 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 177
Software Software Software Name Purpose BUSTER refinement XDS data reduction XDS data scaling MOLREP phasing