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A re-determination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6A resolution using sulphur-SAS at 1.54A wavelength
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 vapor diffusion method 7.2 293 50 mM Tris Buffer, 70% MPD reservoir,17-20Mg/ml prot,5 mM CaCl2 and 60% MPD in the droplet, pH 7.2, vapor diffusion method, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.25 45.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.05 α = 90 b = 46.05 β = 90 c = 101.58 γ = 120
Symmetry Space Group P 31 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 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9A NSLS X9A
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 1.6 19.96 0.059 50.1 12.1 17048
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) 1.6 1.66 0.284 3188
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SULPHUR-SAS THROUGHOUT 1.6 19.96 17048 16184 860 99.66 0.17893 0.17703 0.1758 0.21658 0.2146 RANDOM 24.462
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.62 r_scangle_it 4.071 r_scbond_it 2.569 r_mcangle_it 1.671 r_angle_refined_deg 1.536 r_mcbond_it 0.88 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.62 r_scangle_it 4.071 r_scbond_it 2.569 r_mcangle_it 1.671 r_angle_refined_deg 1.536 r_mcbond_it 0.88 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.173 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.097 r_metal_ion_refined 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 954 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction REFMAC refinement SCALEPACK data scaling