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The crystal structure of Deltarasin in complex with PDE6D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NAL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.8 295 0.1M Na acetate pH3.8, PEG300 29.50%
Crystal Properties Matthews coefficient Solvent content 2.71 54.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.843 α = 90 b = 55.843 β = 90 c = 116.524 γ = 120
Symmetry Space Group P 32 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 EIGER2 XE 16M 2019-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.85 48.36 99.8 0.081 0.086 0.039 0.995 11.8 9 18659
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 1.85 1.88 99.1 1.022 0.484 0.725 1.1 5.2
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 5NAL 1.85 48.36 18615 943 100 0.203 0.203 0.1998 0.216 0.2165 RANDOM 38.13
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] -5.5835 -5.5835 11.1669
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.45 t_omega_torsion 3.79 t_angle_deg 1.07 t_bond_d 0.01 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 16.45 t_omega_torsion 3.79 t_angle_deg 1.07 t_bond_d 0.01 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 1218 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 50
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction DIALS data reduction DIALS data scaling DIMPLE phasing