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Crystal structure of the GP42 transglutaminase from Phytophthora sojae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 11 293 1.6M ammonium sulfate, 0.2M lithium sulfate, 0.1M N-cyclohexyl-3-aminopropanesulfonic acid (CAPS), pH 11.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.71 73.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 195.48 α = 90 b = 195.48 β = 90 c = 137.3 γ = 120
Symmetry Space Group P 62 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 2010-06-28 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2010-02-25 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA 2 SYNCHROTRON SLS BEAMLINE X06DA 1.255 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.95 30 96.4 0.14 0.09 15.5 3.7 33060 31882 -3 -3 42.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.95 3.026 98.2 0.66 0.583 2.75 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SIRAS THROUGHOUT 2.95 30 -3 31882 30288 1594 96.59 0.21584 0.21488 0.23426 0.1999 RANDOM 45.922
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] -1.75 -0.87 -1.75 2.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.281 r_dihedral_angle_3_deg 13.377 r_dihedral_angle_4_deg 9.963 r_dihedral_angle_1_deg 4.461 r_angle_refined_deg 0.889 r_mcangle_it 0.616 r_scangle_it 0.529 r_mcbond_it 0.341 r_scbond_it 0.304 r_chiral_restr 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.281 r_dihedral_angle_3_deg 13.377 r_dihedral_angle_4_deg 9.963 r_dihedral_angle_1_deg 4.461 r_angle_refined_deg 0.889 r_mcangle_it 0.616 r_scangle_it 0.529 r_mcbond_it 0.341 r_scbond_it 0.304 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5227 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose XDS data scaling SHARP phasing REFMAC refinement XDS data reduction XSCALE data scaling