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Plexin A1 full extracellular region, domains 1 to 10, to 4 angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OKT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.5 6% (w/v) PEG 4k,
5 mM tricine or 5 mM TRIS
Crystal Properties Matthews coefficient Solvent content 6.27 76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 195.343 α = 90 b = 195.343 β = 90 c = 176.18 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2011-04-29 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2011-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96131 Diamond I24 2 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.96131 Diamond I04-1
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 87 99.1 0.241 5.2 5.1 28954
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 4 1.04
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 MOLECULAR REPLACEMENT THROUGHOUT 3OKT 4 87.51 27483 1471 98.6 0.259 0.257 0.2526 0.308 0.3033 RANDOM 133.7
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 r_dihedral_angle_2_deg 33.895 r_long_range_B_refined 19.03 r_dihedral_angle_3_deg 18.742 r_dihedral_angle_4_deg 13.529 r_mcangle_it 8.991 r_dihedral_angle_1_deg 7.636 r_scbond_it 5.45 r_mcbond_it 5.114 r_angle_refined_deg 1.243 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.895 r_long_range_B_refined 19.03 r_dihedral_angle_3_deg 18.742 r_dihedral_angle_4_deg 13.529 r_mcangle_it 8.991 r_dihedral_angle_1_deg 7.636 r_scbond_it 5.45 r_mcbond_it 5.114 r_angle_refined_deg 1.243 r_chiral_restr 0.08 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9085 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 607
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing