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Crystal Structure of The Complex of Group 1 Phospholipase A2 With Atropin At 1.5 A Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NJU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 10MM sodium phosphate buffer, 2M calcium chloride, 35% ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.377 α = 90 b = 42.377 β = 90 c = 65.17 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 77 CCD MARRESEARCH Mirror 2010-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
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 1.5 42.4 97 0.058 73.6 18066 18066 23.6
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) 1.5 1.53 91 0.576 2.4
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3NJU 1.5 42.37 18066 17139 925 96.87 0.20078 0.1992 0.22945 0.2545 RANDOM 22.528
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] -0.09 -0.09 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.648 r_dihedral_angle_1_deg 4.341 r_scangle_it 3.657 r_scbond_it 2.279 r_angle_refined_deg 2.174 r_mcangle_it 1.628 r_angle_other_deg 1.221 r_mcbond_it 0.831 r_nbd_refined 0.287 r_symmetry_vdw_refined 0.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.648 r_dihedral_angle_1_deg 4.341 r_scangle_it 3.657 r_scbond_it 2.279 r_angle_refined_deg 2.174 r_mcangle_it 1.628 r_angle_other_deg 1.221 r_mcbond_it 0.831 r_nbd_refined 0.287 r_symmetry_vdw_refined 0.261 r_chiral_restr 0.251 r_symmetry_hbond_refined 0.237 r_symmetry_vdw_other 0.219 r_metal_ion_refined 0.215 r_nbd_other 0.201 r_xyhbond_nbd_refined 0.154 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.009 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 910 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 22
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling