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Crystal structure of the D49 phospholipase A2 piratoxin III from Bothrops pirajai.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CL5 PDB ENTRY 1CL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.3 18% 2-PROPANOL, 21% PEG 4000 AND 0.1 M NA CITRATE PH 5.3
Crystal Properties Matthews coefficient Solvent content 2.32 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.019 α = 90 b = 100.937 β = 123.76 c = 48.333 γ = 90
Symmetry Space Group C 1 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 290 IMAGE PLATE MARRESEARCH 2000-09-15 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 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 2.4 14.7 85.9 0.114 2.9 8166 20.1
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 2.4 2.51 89.6 0.264
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 PDB ENTRY 1CL5 2.4 14.66 8166 423 85.9 0.201 0.201 0.2053 0.255 0.1942 RANDOM 33.5
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] 1.18 11.25 -7.22 6.05
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 7.17 c_scbond_it 5.24 c_mcangle_it 4.51 c_mcbond_it 3.1 c_angle_deg 1.4 c_improper_angle_d 0.8 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 7.17 c_scbond_it 5.24 c_mcangle_it 4.51 c_mcbond_it 3.1 c_angle_deg 1.4 c_improper_angle_d 0.8 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1887 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 8
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing