☰ Navigation Tabs
Crystal Structure of human IDH1 mutant (R132H) in complex with NADP+ and an Inhibitor related to BAY 1436032
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 PROTEIN BUFFER: 15 MG/ML. PROTEIN IN 25 MM HEPES, 300 MM NACL, 5 MM BETA-ME, COMPLETE PROTEASE INHIBITOR MIXTURE, PH 7.7 RESERVOIR: 100
MM BIS-TRIS, PH 7.0, 200 MM CA-ACETATE, 20.0 %(W/V) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.76 55.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.9 α = 90 b = 110.32 β = 91.19 c = 198.54 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 93 PIXEL DECTRIS PILATUS 6M-F 2013-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
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 2.7 30 98.7 0.12 8.6 4.8 56625 2
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 2.7 2.85 99 0.7 2.3 4.8
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 4KZO 2.7 29.94 53784 2839 98.53 0.19722 0.19546 0.1958 0.22977 0.2309 RANDOM 73.2
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] -0.03 0.48 -0.43 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.606 r_dihedral_angle_4_deg 20.556 r_dihedral_angle_3_deg 17.938 r_dihedral_angle_1_deg 6.319 r_long_range_B_refined 5.967 r_long_range_B_other 5.89 r_mcangle_it 2.718 r_mcangle_other 2.718 r_scangle_other 2.571 r_mcbond_it 1.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.606 r_dihedral_angle_4_deg 20.556 r_dihedral_angle_3_deg 17.938 r_dihedral_angle_1_deg 6.319 r_long_range_B_refined 5.967 r_long_range_B_other 5.89 r_mcangle_it 2.718 r_mcangle_other 2.718 r_scangle_other 2.571 r_mcbond_it 1.532 r_mcbond_other 1.532 r_angle_refined_deg 1.484 r_scbond_it 1.454 r_scbond_other 1.454 r_angle_other_deg 1.317 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12995 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 270
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing