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Crystal structure of Western clawed frog MDM2 RING domain homodimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 0.1 M PCTP, 25 % w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.16 42.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.559 α = 90 b = 23.76 β = 101.224 c = 55.744 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 EIGER2 XE 16M 2017-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97997 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.53 41.75 99.8 0.983 3.7 3.1 3830
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.53 2.6 0.652
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7AH2 2.532 41.745 3830 198 99.532 0.22 0.2167 0.2159 0.2788 0.2763 42.802
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] 0.339 0.296 1.592 -1.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.057 r_dihedral_angle_4_deg 25.219 r_dihedral_angle_3_deg 21.365 r_lrange_it 6.951 r_lrange_other 6.948 r_dihedral_angle_1_deg 6.02 r_scangle_it 4.22 r_scangle_other 4.22 r_mcangle_it 4.195 r_mcangle_other 4.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.057 r_dihedral_angle_4_deg 25.219 r_dihedral_angle_3_deg 21.365 r_lrange_it 6.951 r_lrange_other 6.948 r_dihedral_angle_1_deg 6.02 r_scangle_it 4.22 r_scangle_other 4.22 r_mcangle_it 4.195 r_mcangle_other 4.192 r_scbond_it 2.609 r_scbond_other 2.606 r_mcbond_it 2.598 r_mcbond_other 2.598 r_angle_refined_deg 1.377 r_angle_other_deg 1.226 r_symmetry_nbd_refined 0.268 r_nbd_other 0.227 r_symmetry_nbd_other 0.198 r_nbd_refined 0.183 r_nbtor_refined 0.151 r_symmetry_xyhbond_nbd_refined 0.135 r_xyhbond_nbd_refined 0.103 r_ncsr_local_group_1 0.098 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.057 r_metal_ion_refined 0.018 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 822 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing