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Crystal structure of a novel phospholipase A2 from Naja naja sagittifera at 1.5 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PSH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 1mM CaCl2, 35% ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.017 α = 90 b = 42.017 β = 90 c = 64.451 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH Mirror 2003-01-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE CU K-ALPHA 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.477 20.99 0.038 26.6 3.9 17781 17781 20.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.477 1.53 97.5 0.375 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1PSH 1.477 20 17781 17781 586 99.99 0.1904 0.18971 0.18842 0.22961 RANDOM 19.954
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] -0.43 -0.43 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.28 r_dihedral_angle_1_deg 3.958 r_scangle_it 2.955 r_scbond_it 1.979 r_angle_refined_deg 1.798 r_mcangle_it 1.203 r_angle_other_deg 1.076 r_mcbond_it 0.615 r_symmetry_hbond_refined 0.598 r_symmetry_vdw_refined 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.28 r_dihedral_angle_1_deg 3.958 r_scangle_it 2.955 r_scbond_it 1.979 r_angle_refined_deg 1.798 r_mcangle_it 1.203 r_angle_other_deg 1.076 r_mcbond_it 0.615 r_symmetry_hbond_refined 0.598 r_symmetry_vdw_refined 0.29 r_nbd_refined 0.281 r_symmetry_vdw_other 0.28 r_nbd_other 0.21 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.091 r_metal_ion_refined 0.038 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 913 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement MAR345 data collection CCP4 data scaling AMoRE phasing