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Crystal structure of catalytically-active phospholipase A2 with bound calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UMV PDB ENTRY 1UMV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 PEG 3350, CaCl2, tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.72 27.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.206 α = 90 b = 53.218 β = 90 c = 90.057 γ = 90
Symmetry Space Group C 2 2 21
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 MARRESEARCH 2004-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.427 LNLS D03B-MX1
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 1.6 30 99.2 0.047 12748 2 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 1.6 1.63 98.9 0.482
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 (All) 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 PDB ENTRY 1UMV 1.6 22.9 12723 606 99.1 0.205 0.17892 0.1763 0.1796 0.23199 0.2394 RANDOM 24.034
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] 0.25 -0.24 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.026 r_scangle_it 4.022 r_sphericity_free 3.58 r_sphericity_bonded 3.037 r_scbond_it 2.81 r_mcangle_it 2.106 r_angle_refined_deg 1.722 r_rigid_bond_restr 1.465 r_mcbond_it 1.307 r_symmetry_hbond_refined 0.273
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.026 r_scangle_it 4.022 r_sphericity_free 3.58 r_sphericity_bonded 3.037 r_scbond_it 2.81 r_mcangle_it 2.106 r_angle_refined_deg 1.722 r_rigid_bond_restr 1.465 r_mcbond_it 1.307 r_symmetry_hbond_refined 0.273 r_nbd_refined 0.242 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.13 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 950 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing