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Crystal structure of IDH1 R132H mutant in complex with FT-2102
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3INM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG 3000, 0.1 M Sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.62 53.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.328 α = 90 b = 97.825 β = 98.41 c = 75.243 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 PILATUS3 6M 2018-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 2.11 47.66 100 0.07 16.9 6.8 57115
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 2.11 2.15 100 0.69 2.4 6.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3INM 2.11 47.66 57115 2785 100 0.17 0.168 0.22 0.225 RANDOM 52.51
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] 1.5854 -2.2251 0.1726 -1.7579
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.54 t_omega_torsion 3.5 t_angle_deg 1.05 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 15.54 t_omega_torsion 3.5 t_angle_deg 1.05 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 6553 Nucleic Acid Atoms Solvent Atoms 860 Heterogen Atoms 209
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing