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Mouse Semaphorin 3A, domains Sema-PSI-IG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q47
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1M sodium cacodylate, 0.1M calcium acetate, 12% w/v PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.43 64.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.63 α = 90 b = 126.17 β = 90 c = 161.48 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2011-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9173 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.3 99.42 97.7 30776 29876 -3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1Q47 3.3 77 -3 29876 28371 1505 97.14 0.21585 0.21585 0.21321 0.2151 0.26499 0.2647 RANDOM 55.898
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] -0.85 2.49 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.669 r_dihedral_angle_4_deg 18.454 r_dihedral_angle_3_deg 17.074 r_dihedral_angle_1_deg 8.747 r_angle_refined_deg 1.556 r_angle_other_deg 0.901 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.669 r_dihedral_angle_4_deg 18.454 r_dihedral_angle_3_deg 17.074 r_dihedral_angle_1_deg 8.747 r_angle_refined_deg 1.556 r_angle_other_deg 0.901 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8731 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 155
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction Aimless data scaling