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Crystal structure of the Ubl domain of Mdy2 (Get5) at 1.78A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M62 PDB ENTRY 3M62
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 3 M AMMONIUM SULFATE, 100 MM SODIUM CITRATE PH 5.5 MIXED WITH AN EQUAL VOLUME OF PROTEIN AT 6MG/ML, HANGING DROP VAPOUR DIFFUSION.
Crystal Properties Matthews coefficient Solvent content 2.83 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.19 α = 90 b = 47.19 β = 90 c = 78.41 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 100 CCD ADSC CCD 2011-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.78 40.87 99.8 0.06 5.75 7.72 10128
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 1.78 1.88 100 0.35 2.2 7.8
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 3M62 1.78 19.77 9603 486 99.72 0.20327 0.20113 0.2082 0.24825 0.2461 RANDOM 24.108
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.851 r_dihedral_angle_3_deg 14.315 r_dihedral_angle_1_deg 5.925 r_scangle_it 5.358 r_scbond_it 3.576 r_mcangle_it 2.054 r_angle_refined_deg 1.987 r_mcbond_it 1.249 r_angle_other_deg 0.968 r_symmetry_hbond_refined 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.851 r_dihedral_angle_3_deg 14.315 r_dihedral_angle_1_deg 5.925 r_scangle_it 5.358 r_scbond_it 3.576 r_mcangle_it 2.054 r_angle_refined_deg 1.987 r_mcbond_it 1.249 r_angle_other_deg 0.968 r_symmetry_hbond_refined 0.72 r_mcbond_other 0.383 r_nbd_refined 0.221 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.165 r_symmetry_vdw_other 0.155 r_symmetry_vdw_refined 0.15 r_chiral_restr 0.114 r_nbtor_other 0.095 r_bond_refined_d 0.024 r_xyhbond_nbd_other 0.023 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 622 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing