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Crystal Structure of MDMX phosporylated Tyr99 in complex with a 12-mer peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 12% isopropanol, 0.1M MES pH 6.5 and 10% PEG5000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.613 α = 103.32 b = 41.43 β = 103.67 c = 45.618 γ = 102.44
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2013-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.9753 SSRL BL7-1
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 1.55 42.33 93 0.059 16.14 1.9 27683 25745
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 1.55 1.58 87.4 0.485 1.1 1.7 1545
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3EQY 1.55 42.33 26342 24762 1341 94.66 0.18249 0.18249 0.18044 0.1912 0.22034 0.2276 RANDOM 30.003
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] -0.63 -0.54 0.46 -0.16 0.22 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.971 r_dihedral_angle_4_deg 24.265 r_dihedral_angle_3_deg 15.56 r_long_range_B_refined 7.611 r_long_range_B_other 7.523 r_dihedral_angle_1_deg 6.458 r_scangle_other 5.767 r_mcangle_other 3.995 r_mcangle_it 3.988 r_scbond_it 3.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.971 r_dihedral_angle_4_deg 24.265 r_dihedral_angle_3_deg 15.56 r_long_range_B_refined 7.611 r_long_range_B_other 7.523 r_dihedral_angle_1_deg 6.458 r_scangle_other 5.767 r_mcangle_other 3.995 r_mcangle_it 3.988 r_scbond_it 3.854 r_scbond_other 3.851 r_mcbond_it 2.828 r_mcbond_other 2.813 r_angle_refined_deg 1.964 r_angle_other_deg 0.99 r_chiral_restr 0.139 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1514 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling