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Crystal structure of the USP8 interaction domain of human NRDP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 1.8M (NH4)2SO4, 0.1M HEPES pH 7.0,0.2M NaCl, 0.001M DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.1 41.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.796 α = 90 b = 44.262 β = 90 c = 88.339 γ = 90
Symmetry Space Group P 21 21 21
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 SBC-3 2005-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.00769 APS 19-BM
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 1.87 27.36 99 0.14 8.97 4.3 12100 12100 -3
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 1.87 1.94 100 0.653 1.52 4.4 1173
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.87 27.36 10951 549 98.96 0.172 0.16916 0.1701 0.23163 0.2341 RANDOM 15.627
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] -0.47 0.52 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.217 r_dihedral_angle_4_deg 18.452 r_dihedral_angle_3_deg 13.178 r_scangle_it 5.778 r_dihedral_angle_1_deg 5.659 r_scbond_it 3.809 r_mcangle_it 2.51 r_mcbond_it 2.045 r_angle_refined_deg 1.552 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.217 r_dihedral_angle_4_deg 18.452 r_dihedral_angle_3_deg 13.178 r_scangle_it 5.778 r_dihedral_angle_1_deg 5.659 r_scbond_it 3.809 r_mcangle_it 2.51 r_mcbond_it 2.045 r_angle_refined_deg 1.552 r_nbtor_refined 0.306 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.203 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.106 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1047 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing ARP/wARP model building