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Piratoxin-II (Prtx-II) - a K49 PLA2 from Bothrops pirajai
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CLP PDB ENTRY 1CLP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 277 28% PEG 3350, 0.25 M LITHIUM SULFATE 0.1 M TRIS-HCL PH 8.5, AT 277 K FOR APPROX. 40 DAYS
Crystal Properties Matthews coefficient Solvent content 3.17 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.19 α = 90 b = 60.36 β = 96.05 c = 58.74 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 277 IMAGE PLATE MARRESEARCH 1997-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 LNLS D03B-MX1
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 2.04 20 90.2 0.07 12.4 3.43 6934 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.11 72.5 0.26 2.57 1.53
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1CLP 2.04 10 2 23809 1190 90.2 0.176 0.1717 0.268 RANDOM
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 p_planar_d 0.047 p_angle_d 0.038 p_bond_d 0.015 p_angle_deg p_hb_or_metal_coord p_mcbond_it p_mcangle_it p_scbond_it p_scangle_it p_plane_restr
RMS Deviations Key Refinement Restraint Deviation p_planar_d 0.047 p_angle_d 0.038 p_bond_d 0.015 p_angle_deg p_hb_or_metal_coord p_mcbond_it p_mcangle_it p_scbond_it p_scangle_it p_plane_restr p_chiral_restr p_singtor_nbd p_multtor_nbd p_xhyhbond_nbd p_xyhbond_nbd p_planar_tor p_staggered_tor p_orthonormal_tor p_transverse_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1908 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing