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Crystal structure of phospholipase A2 in complex with atropine at 1.23A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SKG pdb entry 1SKG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.2M ammonium sulphate, 30% PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.4 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.331 α = 90 b = 52.331 β = 90 c = 48.071 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 200 CCD MARRESEARCH Mirror 2004-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.803 EMBL/DESY, HAMBURG X11
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 1.23 51.99 99.82 0.053 33.2 37504 37504
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.23 1.25 100 3.7
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1SKG 1.23 51.99 37504 36667 767 99.82 0.18909 0.18877 0.20444 RANDOM 14.146
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] 0.19 0.19 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.451 r_dihedral_angle_1_deg 3.975 r_scangle_it 2.164 r_angle_refined_deg 1.946 r_scbond_it 1.399 r_mcangle_it 1.191 r_angle_other_deg 0.79 r_mcbond_it 0.635 r_nbd_refined 0.435 r_symmetry_hbond_refined 0.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.451 r_dihedral_angle_1_deg 3.975 r_scangle_it 2.164 r_angle_refined_deg 1.946 r_scbond_it 1.399 r_mcangle_it 1.191 r_angle_other_deg 0.79 r_mcbond_it 0.635 r_nbd_refined 0.435 r_symmetry_hbond_refined 0.235 r_nbd_other 0.213 r_chiral_restr 0.211 r_xyhbond_nbd_refined 0.21 r_symmetry_vdw_refined 0.2 r_symmetry_vdw_other 0.162 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 943 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing