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Crystal structure of the DUB domain of human AMSH-LP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 45mM sodium acetate buffer (pH 4.6), 22% PEG 4000, 90mM ammonium acetate, 10mM praseodymium (III) acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.13 60.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.865 α = 90 b = 81.865 β = 90 c = 64.693 γ = 120
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 QUANTUM 210 mirrors 2008-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00000 Photon Factory AR-NW12A
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 1.2 70.89 99.4 0.046 34.3 76845 76845
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) 1.2 1.21 98.3 0.158 14.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 1.2 31.09 76845 72536 3830 99.37 0.14962 0.14879 0.1478 0.16546 0.1644 RANDOM 13.235
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] 0.57 0.29 0.57 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.57 r_dihedral_angle_3_deg 11.334 r_dihedral_angle_4_deg 8.306 r_dihedral_angle_1_deg 5.972 r_sphericity_free 4.374 r_sphericity_bonded 4.158 r_scangle_it 3.012 r_scbond_it 2.165 r_mcangle_it 1.817 r_angle_refined_deg 1.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.57 r_dihedral_angle_3_deg 11.334 r_dihedral_angle_4_deg 8.306 r_dihedral_angle_1_deg 5.972 r_sphericity_free 4.374 r_sphericity_bonded 4.158 r_scangle_it 3.012 r_scbond_it 2.165 r_mcangle_it 1.817 r_angle_refined_deg 1.261 r_rigid_bond_restr 1.249 r_mcbond_it 1.215 r_nbtor_refined 0.307 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.196 r_symmetry_vdw_refined 0.192 r_chiral_restr 0.081 r_symmetry_hbond_refined 0.076 r_metal_ion_refined 0.053 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1432 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling SHARP phasing