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Crystal structure analysis of a basic phospholipase A2 from Trimeresurus stejnegeri venom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B4W PDB ENTRY 1B4W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 287 2.2 M sodium chloride, 16% PEG6000, 0.015 mM CYMAL-7, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 1.94 36.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.946 α = 90 b = 71.436 β = 103.53 c = 53.607 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 2010-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 0.97916
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 1.55 50 99.9 51060 50982
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 1.55 1.61 100 0.433 0.348 3.9 5.6 5105
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 1B4W 1.55 30 48372 2587 99.77 0.18311 0.18093 0.1785 0.22316 0.2207 RANDOM 26.282
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] -0.33 1.35 -0.67 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.6 r_dihedral_angle_4_deg 14.698 r_dihedral_angle_3_deg 12.078 r_scangle_it 5.245 r_dihedral_angle_1_deg 4.855 r_mcangle_it 3.627 r_scbond_it 3.558 r_mcbond_it 2.128 r_angle_refined_deg 1.066 r_rigid_bond_restr 1.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.6 r_dihedral_angle_4_deg 14.698 r_dihedral_angle_3_deg 12.078 r_scangle_it 5.245 r_dihedral_angle_1_deg 4.855 r_mcangle_it 3.627 r_scbond_it 3.558 r_mcbond_it 2.128 r_angle_refined_deg 1.066 r_rigid_bond_restr 1.015 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 2599 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 5
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling