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Crystal Structure of the ubiquitin-like domain of plexin D1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 298 1.39M sodium citrate, 0.1M sodium cacodylate. The protein stock solution was adjusted to contain 15 mM TCEP, supplemented with 1:100 (w/w) chymotrypsin, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.777 α = 90 b = 27.051 β = 114.06 c = 52.653 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315 2009-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97942 APS 19-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 30 99.5 0.086 9.6 4.4 7245
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) 2 2.03 99.7 0.499 3.6 381
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 SAD THROUGHOUT 2.004 30 7229 337 98.865 0.244 0.243 0.2381 0.276 0.2699 RANDOM 31.154
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] -1.706 -0.265 1.444 0.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.446 r_dihedral_angle_4_deg 20.348 r_dihedral_angle_3_deg 14.389 r_dihedral_angle_1_deg 6.012 r_scangle_it 1.814 r_mcangle_it 1.651 r_scbond_it 1.305 r_angle_refined_deg 1.095 r_mcbond_it 0.983 r_angle_other_deg 0.748
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.446 r_dihedral_angle_4_deg 20.348 r_dihedral_angle_3_deg 14.389 r_dihedral_angle_1_deg 6.012 r_scangle_it 1.814 r_mcangle_it 1.651 r_scbond_it 1.305 r_angle_refined_deg 1.095 r_mcbond_it 0.983 r_angle_other_deg 0.748 r_mcbond_other 0.217 r_chiral_restr 0.062 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 775 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 3
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction