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SP2-SP3 - a complex of two storage proteins from Bombyx mori hemolymph
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GWJ PDB ENTRY 3GWJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 2.0 M ammonium sulfate
0.02 M sodium thiocyanate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.97 58.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.75 α = 90 b = 192.75 β = 90 c = 180.82 γ = 120
Symmetry Space Group P 63 2 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 CCD MARMOSAIC 225 mm CCD mirrors 2012-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918 BESSY 14.2
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 2.9 48 99.7 0.108 23.2 10.2 44365 44232 -3 43.07
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 2.9 3 100 0.639 5 10.5 4198
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 ENTRY 3GWJ 2.9 48 44365 43121 1096 99.65 0.16726 0.16726 0.16582 0.1659 0.22267 0.2222 RANDOM 51.406
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] 1.49 1.49 1.49 -4.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.564 r_dihedral_angle_3_deg 19.878 r_dihedral_angle_4_deg 18.281 r_dihedral_angle_1_deg 6.924 r_angle_refined_deg 1.666 r_chiral_restr 0.115 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11373 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 150
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction