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Structure of PIN domain of human SMG5.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HWW PDB Entry: 2HWW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 20% PEG 4000, 100 mM citrate pH 5.5 , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.591 α = 90 b = 42.534 β = 95.98 c = 65.103 γ = 90
Symmetry Space Group P 1 21 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 MAR CCD 165 mm 2004-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.979 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.75 30 98.8 0.065 3.2 6552 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.75 2.9 98.8 0.327 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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: 2HWW 2.75 30 6634 6050 495 98.78 0.27092 0.27534 0.27092 0.2985 0.32882 0.3701 RANDOM 27.264
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] -1.99 -1.38 -0.54 2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.847 r_dihedral_angle_4_deg 20.911 r_dihedral_angle_3_deg 19.676 r_dihedral_angle_1_deg 7.112 r_angle_refined_deg 1.366 r_scangle_it 1.241 r_angle_other_deg 1.053 r_scbond_it 0.863 r_mcangle_it 0.556 r_mcbond_it 0.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.847 r_dihedral_angle_4_deg 20.911 r_dihedral_angle_3_deg 19.676 r_dihedral_angle_1_deg 7.112 r_angle_refined_deg 1.366 r_scangle_it 1.241 r_angle_other_deg 1.053 r_scbond_it 0.863 r_mcangle_it 0.556 r_mcbond_it 0.461 r_symmetry_vdw_refined 0.248 r_symmetry_vdw_other 0.238 r_nbd_refined 0.216 r_nbtor_refined 0.188 r_nbd_other 0.173 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.129 r_symmetry_hbond_refined 0.101 r_nbtor_other 0.088 r_mcbond_other 0.065 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1816 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing