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Crystal Structure Analysis of the human Tub protein (isoform a) spanning residues 289 through 561
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C8Z PDB ENTRY 1C8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277.2 16% PEG 400, 5mM Magnesium Chloride, 100mM Sodium Acetate, 15mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277.2K, pH 5.0
Crystal Properties Matthews coefficient Solvent content 4.56 73.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.981 α = 90 b = 149.981 β = 90 c = 149.981 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARRESEARCH 2003-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 0.9814 APS 32-ID
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 2.7 20 100 0.096 30.9 24 15560 15503 -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 2.7 2.8 99.7 100 0.344 10.1 1511
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 (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 1C8Z 2.704 18.474 14674 14674 767 100 0.1836 0.1814 0.1875 0.2264 0.23 Random 33.802
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]
RMS Deviations Key Refinement Restraint Deviation Torsion angles, period 2. refined 35.395 Torsion angles, period 4. refined 21.636 Torsion angles, period 3. refined 20.368 Torsion angles, period 1. refined 7.722 S. chain angle B values: refined atoms 3.361 S. chain bond B values: refined atoms 1.952 M. chain angle B values: refined atoms 1.903 Bond angles : refined atoms 1.612 S. chain angle B values: others 1.468 M. chain bond B values: refined atoms 1.08
RMS Deviations Key Refinement Restraint Deviation Torsion angles, period 2. refined 35.395 Torsion angles, period 4. refined 21.636 Torsion angles, period 3. refined 20.368 Torsion angles, period 1. refined 7.722 S. chain angle B values: refined atoms 3.361 S. chain bond B values: refined atoms 1.952 M. chain angle B values: refined atoms 1.903 Bond angles : refined atoms 1.612 S. chain angle B values: others 1.468 M. chain bond B values: refined atoms 1.08 M. chain angle B values: others 0.948 Bond angles : others 0.899 S. chain bond B values: others 0.641 VDW repulsions; symmetry: others 0.282 VDW repulsions; symmetry: refined atoms 0.271 VDW repulsions: refined atoms 0.226 VDW repulsions: others 0.2 VDW; torsion: refined atoms 0.184 HBOND: refined atoms 0.146 M. chain bond B values: others 0.138 HBOND; symmetry: refined atoms 0.121 Chiral centres: refined atoms 0.099 VDW; torsion: others 0.095 Bond distances: refined atoms 0.017 Planar groups: refined atoms 0.005 Bond distances: others 0.001 Planar groups: others 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2138 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement