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Structure of Oryza Sativa (Rice) PLA2, orthorhombic crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other P62 CRYSTAL FORM
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 2.48 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.094 α = 90 b = 41.491 β = 90 c = 53.124 γ = 90
Symmetry Space Group P 21 21 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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.3 30 94.7 0.01 17.4 4.8 15584 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 2.3 2.42 93.2 0.33 5.4 4.9
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 P62 CRYSTAL FORM 2.3 30 15584 846 94.72 0.19271 0.1898 0.1888 0.24505 0.2397 RANDOM 26.486
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] -0.6 -0.09 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.581 r_dihedral_angle_3_deg 13.209 r_dihedral_angle_4_deg 10.666 r_dihedral_angle_1_deg 4.973 r_scangle_it 2.092 r_scbond_it 1.296 r_angle_refined_deg 1.195 r_mcangle_it 0.755 r_mcbond_it 0.394 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.581 r_dihedral_angle_3_deg 13.209 r_dihedral_angle_4_deg 10.666 r_dihedral_angle_1_deg 4.973 r_scangle_it 2.092 r_scbond_it 1.296 r_angle_refined_deg 1.195 r_mcangle_it 0.755 r_mcbond_it 0.394 r_nbtor_refined 0.292 r_symmetry_vdw_refined 0.192 r_nbd_refined 0.189 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.141 r_metal_ion_refined 0.131 r_chiral_restr 0.07 r_bond_refined_d 0.009 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 2459 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing