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Structure of the Symmetric Mad2 Dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KLQ PDB ENTRY 1KLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 VAPOR DIFFUSION, HANGING DROP, 20 DEGREES C. 1 MICROLITER PROTEIN: 3 MG/ML IN 20 MM TRIS, PH 8.0, 50 MM NACL, 2 MM TCEP PLUS 1 MICROLITER RESERVOIR: 19% PEG2000, 16% GLYCEROL, 100 MM TRIS, PH 8.0, 0.3 M MGCL2
Crystal Properties Matthews coefficient Solvent content 2.9 57.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.337 α = 90 b = 191.407 β = 90.02 c = 154.307 γ = 90
Symmetry Space Group C 1 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 100 CCD ADSC CCD 2006-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 1.95 45.37 97.7 0.07 14.9 2.9 223558 -3 23.5
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 1.95 1.98 95.7 0.55 1.6 2.6
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 PDB ENTRY 1KLQ 1.95 45 220725 2700 97.3 0.209 0.208 0.2071 0.247 0.2437 RANDOM 25.39
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] 0.81 0.2 -0.83 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.022 r_dihedral_angle_4_deg 18.857 r_dihedral_angle_3_deg 14.773 r_scangle_it 2.877 r_dihedral_angle_1_deg 2.008 r_scbond_it 1.788 r_angle_refined_deg 1.501 r_mcangle_it 1.156 r_mcbond_it 0.706 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.022 r_dihedral_angle_4_deg 18.857 r_dihedral_angle_3_deg 14.773 r_scangle_it 2.877 r_dihedral_angle_1_deg 2.008 r_scbond_it 1.788 r_angle_refined_deg 1.501 r_mcangle_it 1.156 r_mcbond_it 0.706 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.211 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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_other r_long_range_B_refined 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 19613 Nucleic Acid Atoms Solvent Atoms 1591 Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing