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Crystal structure of Plexin inhibitor complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 0.1M tri-sodium citrate, 13% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.53 51.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.426 α = 90 b = 217.924 β = 115.3 c = 106.475 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 RAYONIX MX225HE KB mirror 2014-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.6 50 97.2 0.15 0.57 10 3 116573 58.7
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 2.6 2.64 88.7 0.737 1.21 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3OL2 2.6 40.805 1.35 113157 5686 97.11 0.2266 0.2245 0.2653 0.2523 Random selection
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 f_dihedral_angle_d 16.293 f_angle_d 1.014 f_chiral_restr 0.055 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21089 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 98
Software Software Software Name Purpose PHENIX refinement DENZO data collection SCALEPACK data scaling PHASER phasing