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Crystal structure of allergen protein scam1 from Scadoxus multiflorus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O9N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 298 0.1M sodium acetate, 20% PEG 6000, VAPOR DIFFUSION, HANGING DROP, pH 7.2, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.736 α = 90 b = 65.265 β = 102.26 c = 49.32 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 298 IMAGE PLATE MARRESEARCH Mirror 2013-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.514
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 65.26 100 0.064 7.8 15078
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 3O9N 2.2 65.2 12838 667 99.4 0.15545 0.15334 0.1521 0.19618 0.1966 RANDOM 29.726
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] -0.11 0.16 0.17 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.507 r_dihedral_angle_4_deg 26.47 r_dihedral_angle_3_deg 16.141 r_dihedral_angle_1_deg 8.267 r_angle_refined_deg 1.724 r_chiral_restr 0.114 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_mcbond_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2094 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 5
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling