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Crystal structure of a novel Arg49 phospholipase A2 homologue from Zhaoermia mangshanensis venom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y4L PDB ENTRY 1Y4L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 polyethylene glycol 8,000;
ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.57 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.933 α = 90 b = 72.933 β = 90 c = 93.938 γ = 120
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 MAR CCD 165 mm 2007-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.427 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 2.05 23.87 99.5 0.071 33.4 12.5 17731 2
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 2.05 2.12 99.4 0.33 2.8 9.5
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 1Y4L 2.05 23.87 15931 1800 99.51 0.21729 0.20942 0.2054 0.2886 0.2768 RANDOM 29.077
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] 0.98 0.49 0.98 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.521 r_dihedral_angle_3_deg 19.202 r_dihedral_angle_4_deg 15.45 r_dihedral_angle_1_deg 13.676 r_scangle_it 4.163 r_scbond_it 3.068 r_angle_refined_deg 2.223 r_mcangle_it 1.829 r_mcbond_it 1.127 r_nbtor_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.521 r_dihedral_angle_3_deg 19.202 r_dihedral_angle_4_deg 15.45 r_dihedral_angle_1_deg 13.676 r_scangle_it 4.163 r_scbond_it 3.068 r_angle_refined_deg 2.223 r_mcangle_it 1.829 r_mcbond_it 1.127 r_nbtor_refined 0.328 r_symmetry_hbond_refined 0.309 r_nbd_refined 0.245 r_symmetry_vdw_refined 0.234 r_xyhbond_nbd_refined 0.223 r_chiral_restr 0.138 r_bond_refined_d 0.023 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1940 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing