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Crystal structure of phospholipase A2 with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 2.2M Sodium chloride, 0.1M BIS-TRIS propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.44 64.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.726 α = 90 b = 61.063 β = 90 c = 63.356 γ = 90
Symmetry Space Group P 21 2 2
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 OXFORD RUBY CCD 2015-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OXFORD DIFFRACTION ENHANCE ULTRA 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.8 18.78 99.9 0.06 0.064 0.02 0.999 24.8 9.5 18109
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 98.9 0.448 0.495 0.207 0.88 5.6
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 5WZM 1.8 18.78 17182 913 99.78 0.1942 0.1926 0.1992 0.225 0.2259 RANDOM 22.551
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 0.26 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.082 r_dihedral_angle_4_deg 15.79 r_dihedral_angle_3_deg 13.503 r_dihedral_angle_1_deg 4.849 r_angle_refined_deg 1.617 r_angle_other_deg 1.038 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.082 r_dihedral_angle_4_deg 15.79 r_dihedral_angle_3_deg 13.503 r_dihedral_angle_1_deg 4.849 r_angle_refined_deg 1.617 r_angle_other_deg 1.038 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 951 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 63
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction MOLREP phasing