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Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GYD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 15-25% PEG 3350, 400 mM ammonium phosphate, 3.5 mM Mega-10
Crystal Properties Matthews coefficient Solvent content 5.11 75.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.02 α = 90 b = 116.02 β = 90 c = 161.66 γ = 120
Symmetry Space Group P 32 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 83 PIXEL DECTRIS PILATUS3 6M 2011-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 4.1 85.3 99.5 0.115 9.4 7.4 10272 143.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.1 4.21 99.7 1.05 0.981 0.958 2 7.5
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 5GYD 4.1 85.34 9220 1026 99.53 0.24308 0.24187 0.2526 0.25379 0.2809 RANDOM 263.699
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] 10.55 5.28 10.55 -34.23
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 40.847 r_dihedral_angle_2_deg 38.502 r_mcangle_it 29.672 r_scbond_it 22.811 r_mcbond_it 19.155 r_dihedral_angle_3_deg 18.712 r_dihedral_angle_4_deg 15.942 r_dihedral_angle_1_deg 6.832 r_angle_refined_deg 1.531 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 40.847 r_dihedral_angle_2_deg 38.502 r_mcangle_it 29.672 r_scbond_it 22.811 r_mcbond_it 19.155 r_dihedral_angle_3_deg 18.712 r_dihedral_angle_4_deg 15.942 r_dihedral_angle_1_deg 6.832 r_angle_refined_deg 1.531 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3424 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing