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Crystal structure of AhV_bPA, a basic PLA2 from Agkistrodon halys pallas venom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JIA PDB ENTRY 1JIA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 287 18% MPEG5000, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 2.42 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.953 α = 90 b = 53.959 β = 111.48 c = 108.433 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 100 IMAGE PLATE MAR scanner 345 mm plate 2009-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 0.97924 BSRF 3W1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 50 97.2 2.8 70300 68360
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 1.6 1.66 90.8 0.343 0.329 2.7 2.3 6357
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 1JIA 1.6 29 62978 5322 96.99 0.17258 0.17085 0.1689 0.19272 0.1931 RANDOM 30.035
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] -0.53 -0.05 -1.4 1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.109 r_dihedral_angle_4_deg 14.743 r_dihedral_angle_3_deg 12.874 r_scangle_it 5.65 r_dihedral_angle_1_deg 5.05 r_mcangle_it 3.833 r_scbond_it 3.527 r_mcbond_it 2.149 r_rigid_bond_restr 1.948 r_angle_refined_deg 1.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.109 r_dihedral_angle_4_deg 14.743 r_dihedral_angle_3_deg 12.874 r_scangle_it 5.65 r_dihedral_angle_1_deg 5.05 r_mcangle_it 3.833 r_scbond_it 3.527 r_mcbond_it 2.149 r_rigid_bond_restr 1.948 r_angle_refined_deg 1.219 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3744 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 68
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling