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Crystal Structure of BnSP-6, a Lys49-Phospholipase A2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other BthTX-I (closed form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 PEG 6000, ammonium sulphate, sodium cacodilate., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.28 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.67 α = 90 b = 57.67 β = 90 c = 130.13 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 283 IMAGE PLATE MARRESEARCH 1999-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.38 LNLS D03B-MX1
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 2.5 30 91.1 0.136 8.6 11.3 9269 8429 -3 35.8
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) 2.5 2.6 90.2 0.463 1.6 3.3 885
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-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT BthTX-I (closed form) 2.5 26.4 8389 430 91.6 0.186 0.255 random 40.3
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 c_dihedral_angle_d 21.9 c_angle_deg 1.4 c_improper_angle_d 0.81 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1864 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement