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Crystal Structure Analysis of Zebra fish MDMX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N5T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100mM Tris-8.0, 2.4M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.41 48.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.29 α = 90 b = 108.93 β = 90 c = 30.91 γ = 90
Symmetry Space Group C 2 2 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 DECTRIS PILATUS 6M-F 2018-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.25 54.47 99.5 0.073 0.028 11.3 6.5 38363 14.565
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 99.9 1.783 0.7 1.1 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4N5T 1.25 54.465 1.34 38348 1909 99.45 0.1707 0.1694 0.172 0.1962 0.1971 26.7134
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 2.6 f_angle_d 0.826 f_chiral_restr 0.082 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 849 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 5
Software Software Software Name Purpose xia2 data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing