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Crystal structure of deubiquitinase MINDY-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Partial model obatined from experimental phasing
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 100mM Hepes-Na pH 7.5, 200mM NaCl and 25% PEG4000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.671 α = 90 b = 99.671 β = 90 c = 165.123 γ = 90
Symmetry Space Group P 41 2 2
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 2015-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.93927 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3 99.67 99.8 0.065 0.998 14.4 5 17325
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.18 99.9 0.88 0.866 2.1 5.2
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 Partial model obatined from experimental phasing 3 99.67 16430 856 99.7 0.19907 0.19686 0.1997 0.24231 0.2471 RANDOM 118.197
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] 5.56 5.56 -11.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.913 r_dihedral_angle_3_deg 15.245 r_long_range_B_refined 12.826 r_long_range_B_other 12.824 r_dihedral_angle_4_deg 10.037 r_mcangle_it 9.334 r_mcangle_other 9.33 r_scangle_other 9.207 r_dihedral_angle_1_deg 6.245 r_mcbond_it 5.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.913 r_dihedral_angle_3_deg 15.245 r_long_range_B_refined 12.826 r_long_range_B_other 12.824 r_dihedral_angle_4_deg 10.037 r_mcangle_it 9.334 r_mcangle_other 9.33 r_scangle_other 9.207 r_dihedral_angle_1_deg 6.245 r_mcbond_it 5.779 r_mcbond_other 5.759 r_scbond_it 5.572 r_scbond_other 5.567 r_angle_refined_deg 1.204 r_angle_other_deg 0.882 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2002 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing