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Crystal structure of m2hTDP2-CAT in complex with a small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Bis-Tris propane pH 7.5,
0.2 M sodium citrate,
20% w/v PEG3350,
0.3% v/v DMSO
Crystal Properties Matthews coefficient Solvent content 2.5 50.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.01 α = 90 b = 42.8 β = 94.15 c = 108.76 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 PILATUS 6M-F 2013-10-12 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) 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 1.8 42.8 98 0.051 0.87 9.7 2.9 51393 21.69
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 1.8 1.84 79.7 0.166 2 2.1
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 4GYZ 1.8 39.81 51379 2611 97.94 0.174 0.1726 0.1782 0.2023 0.208 RANDOM 26.43
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] 2.9739 -2.6923 -0.2711 -2.7028
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.38 t_other_torsion 2.78 t_angle_deg 0.98 t_bond_d 0.008 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_omega_torsion 3.38 t_other_torsion 2.78 t_angle_deg 0.98 t_bond_d 0.008 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 3992 Nucleic Acid Atoms Solvent Atoms 604 Heterogen Atoms 168
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing