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Structural insights into substrate binding of brown spider venom class II phospholipases D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1 M Tris-HCl pH 7.5, 40% PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.97 37.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.761 α = 90 b = 49.341 β = 105.71 c = 56.152 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 200 CCD MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.458 LNLS W01B-MX2
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 24.49 47089
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.64 24.49 29302 1569 95.54 0.18156 0.17965 0.1858 0.21592 0.216 RANDOM 24.91
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] -0.1 -0.17 0.05 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.861 r_dihedral_angle_3_deg 14.442 r_dihedral_angle_4_deg 12.852 r_long_range_B_refined 7.058 r_dihedral_angle_1_deg 6.254 r_scbond_it 3.164 r_mcangle_it 2.881 r_mcbond_it 2.177 r_angle_refined_deg 2.035 r_chiral_restr 0.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.861 r_dihedral_angle_3_deg 14.442 r_dihedral_angle_4_deg 12.852 r_long_range_B_refined 7.058 r_dihedral_angle_1_deg 6.254 r_scbond_it 3.164 r_mcangle_it 2.881 r_mcbond_it 2.177 r_angle_refined_deg 2.035 r_chiral_restr 0.151 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2183 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 50
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling