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Crystal structure of the cytoplasmic domain of human plexin B1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other For phasing, native crystals were incubated over-night in an artificial mother liquor containing 0.001 M thimerosal.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 16% peg-2000 mme, 0.1M TRIS, 0.2M TMAO, pH 8, vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.39 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.346 α = 90 b = 74.346 β = 90 c = 214.398 γ = 120
Symmetry Space Group P 31 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 2007-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9999 NSLS X25
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 2.4 30 99.9 0.045 15 9.8 27657
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 2.4 2.49 99.9 0.577 7.6 2703
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 For phasing, native crystals were incubated over-night in an artificial mother liquor containing 0.001 M thimerosal. 2.402 28.083 27598 1390 99.779 0.228 0.227 0.2909 0.262 0.3106 RANDOM 47.297
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] 0.953 0.476 0.953 -1.429
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.655 r_dihedral_angle_4_deg 17.721 r_dihedral_angle_3_deg 14.896 r_dihedral_angle_1_deg 5.576 r_mcangle_it 2.886 r_scangle_it 2.695 r_mcbond_it 1.932 r_scbond_it 1.923 r_angle_refined_deg 1.213 r_angle_other_deg 0.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.655 r_dihedral_angle_4_deg 17.721 r_dihedral_angle_3_deg 14.896 r_dihedral_angle_1_deg 5.576 r_mcangle_it 2.886 r_scangle_it 2.695 r_mcbond_it 1.932 r_scbond_it 1.923 r_angle_refined_deg 1.213 r_angle_other_deg 0.899 r_mcbond_other 0.454 r_symmetry_vdw_other 0.274 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.196 r_nbd_other 0.177 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.088 r_nbtor_other 0.087 r_chiral_restr 0.068 r_bond_refined_d 0.013 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 4078 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 19
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling