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Structure of Oryza Sativa (Rice) PLA2, complex with octanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other NATIVE P62 STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 VAPOUR DIFFUSION, 20 DEGREES. WELL CONTAINED 0.75ML OF SOLN A (16-18% PEG3350, 0.1M BISTRISPROPANE PH 6.5, 0.2M POTASSIUM THIOCYANATE) AND 0.25ML OF SOLN B (0.1M SODIUM ACETATE PH 4.6, 2M SODIUM CHLORIDE)
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.159 α = 90 b = 109.159 β = 90 c = 41.394 γ = 120
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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2 30 98.4 0.07 12.6 3.8 18061 2
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 2 2.11 90.8 0.24 4.2 2.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT NATIVE P62 STRUCTURE 2 27.05 18061 963 98.47 0.18833 0.18656 0.22043 0.2305 RANDOM 21.673
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] 0.56 0.28 0.56 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.259 r_dihedral_angle_3_deg 11.511 r_dihedral_angle_4_deg 11.206 r_dihedral_angle_1_deg 4.647 r_scangle_it 2.252 r_scbond_it 1.318 r_mcangle_it 1.07 r_angle_refined_deg 1.005 r_mcbond_it 0.573 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.259 r_dihedral_angle_3_deg 11.511 r_dihedral_angle_4_deg 11.206 r_dihedral_angle_1_deg 4.647 r_scangle_it 2.252 r_scbond_it 1.318 r_mcangle_it 1.07 r_angle_refined_deg 1.005 r_mcbond_it 0.573 r_nbtor_refined 0.292 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.172 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.125 r_metal_ion_refined 0.113 r_chiral_restr 0.061 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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_other r_long_range_B_refined 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 1714 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing