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Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CLS PDB entries 2CLS,2R2O experimental model PDB 2R2O PDB entries 2CLS,2R2O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% PEG 3350, 0.2M Calcium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.05 59.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.136 α = 90 b = 71.653 β = 128.36 c = 101.885 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 100 CCD ADSC QUANTUM 270 2007-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.91790 CHESS F1
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 2.3 30 97.3 0.06 9.1 3.7 36932
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 2.3 2.38 84.8 0.231 3.2 3232
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 entries 2CLS,2R2O 2.3 20 36863 36863 999 97.472 0.216 0.216 0.215 0.2583 0.248 0.2765 Thin shells 28.565
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] 5.87 2.92 -2.831 0.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.303 r_dihedral_angle_4_deg 22.082 r_dihedral_angle_3_deg 14.752 r_dihedral_angle_1_deg 6.345 r_scangle_it 2.327 r_scbond_it 1.508 r_angle_refined_deg 1.448 r_angle_other_deg 0.949 r_mcangle_it 0.936 r_mcbond_it 0.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.303 r_dihedral_angle_4_deg 22.082 r_dihedral_angle_3_deg 14.752 r_dihedral_angle_1_deg 6.345 r_scangle_it 2.327 r_scbond_it 1.508 r_angle_refined_deg 1.448 r_angle_other_deg 0.949 r_mcangle_it 0.936 r_mcbond_it 0.595 r_symmetry_vdw_refined 0.4 r_symmetry_vdw_other 0.197 r_metal_ion_refined 0.196 r_nbd_refined 0.191 r_nbd_other 0.19 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.143 r_mcbond_other 0.128 r_symmetry_hbond_refined 0.124 r_nbtor_other 0.087 r_chiral_restr 0.081 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4279 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 98
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling