☰ Navigation Tabs
Crystal Structure of the complex formed between russells viper phospholipase A2 and a designed peptide inhibitor PHQ-Leu-Val-Arg-Tyr at 1.2A 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, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.48 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.496 α = 90 b = 52.496 β = 90 c = 47.93 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 2004-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.981 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 1.2 30 100 0.077 20.1 5.8 35174 10.5
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 1.2 1.27 99.4 0.454 2.2
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 PDB entry 1skg 1.25 29.36 35174 35174 921 100 0.1884 0.1884 0.18816 0.1971 RANDOM 12.325
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 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.731 r_dihedral_angle_1_deg 6.902 r_scangle_it 2.243 r_angle_refined_deg 2.026 r_scbond_it 1.454 r_mcangle_it 1.2 r_angle_other_deg 1.046 r_mcbond_it 0.648 r_nbd_refined 0.434 r_nbd_other 0.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.731 r_dihedral_angle_1_deg 6.902 r_scangle_it 2.243 r_angle_refined_deg 2.026 r_scbond_it 1.454 r_mcangle_it 1.2 r_angle_other_deg 1.046 r_mcbond_it 0.648 r_nbd_refined 0.434 r_nbd_other 0.245 r_symmetry_vdw_other 0.237 r_symmetry_vdw_refined 0.235 r_symmetry_hbond_refined 0.217 r_xyhbond_nbd_refined 0.195 r_xyhbond_nbd_other 0.119 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 982 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing