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Crystal structure of a complex of phospholipase A2 with a gramine derivative at 2.2 resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PYC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 Ammoniumu acetate, PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.07 α = 90 b = 53.07 β = 90 c = 48.5 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 291 IMAGE PLATE MAR scanner 345 mm plate Mirror 2007-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54132
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 2.2 18.06 97 0.093 6619 6606 32.7
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) 2.2 2.29 92 0.226
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PYC 2.21 18.06 6619 6606 370 96.7 0.176 0.176 0.1813 0.189 0.2193 RANDOM 30.8
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] 1.28 1.28 -2.55
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24 c_scangle_it 3.66 c_mcangle_it 2.79 c_scbond_it 2.46 c_mcbond_it 1.7 c_angle_deg 1.6 c_improper_angle_d 0.76 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24 c_scangle_it 3.66 c_mcangle_it 2.79 c_scbond_it 2.46 c_mcbond_it 1.7 c_angle_deg 1.6 c_improper_angle_d 0.76 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 944 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 17
Software Software Software Name Purpose CNS refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing