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HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 16 AT 1.20A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q9Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 2.5M AmSO4, 0.1M KSCN, 1% v/v MPD, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 2.05 39.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.492 α = 90 b = 42.426 β = 90 c = 107.421 γ = 90
Symmetry Space Group P 21 21 21
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 PSI PILATUS 6M 2013-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.2 19.73 99.9 0.035 0.039 1 25.7 6.2 60131 16.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.23 99.2 0.517 0.571 0.871 3.4 5.5
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 6Q9Q 1.2 19.73 57124 3007 99.89 0.162 0.1608 0.1588 0.1842 0.1812 RANDOM 14.678
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] 0.01 0.04 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.079 r_dihedral_angle_4_deg 11.53 r_dihedral_angle_3_deg 11.023 r_dihedral_angle_1_deg 5.876 r_sphericity_free 4.242 r_sphericity_bonded 3.546 r_rigid_bond_restr 1.436 r_angle_refined_deg 1.268 r_chiral_restr 0.095 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.079 r_dihedral_angle_4_deg 11.53 r_dihedral_angle_3_deg 11.023 r_dihedral_angle_1_deg 5.876 r_sphericity_free 4.242 r_sphericity_bonded 3.546 r_rigid_bond_restr 1.436 r_angle_refined_deg 1.268 r_chiral_restr 0.095 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1381 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 52
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction