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Structure of a fragment of human phospholipase C-beta3 delta472-581, bound to IP3 and in complex with Galphaq
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OHM PDB ENTRY 3OHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.25 277.15 100 mM MES, 200 mM NaCl, 5% (v/v) PEG 3350, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 3.13 60.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 205.918 α = 90 b = 89.869 β = 101.8 c = 93.261 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARMOSAIC 300 mm CCD 2014-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.979 APS 21-ID-D
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 3.4 30 96.1 0.142 7.695 3 27361 22003 -2000 -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 3.4 3.46 95.9 0.44 2.05 2.8
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 PDB ENTRY 3OHM 3.41 29.34 20962 20962 1040 95.49 0.21502 0.21189 0.212 0.27671 0.2746 RANDOM 84.894
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] -1.37 -0.03 1.69 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.353 r_dihedral_angle_3_deg 15.665 r_dihedral_angle_4_deg 13.79 r_dihedral_angle_1_deg 5.623 r_long_range_B_refined 2.64 r_long_range_B_other 2.64 r_mcangle_it 1.528 r_mcangle_other 1.528 r_angle_refined_deg 1.016 r_scangle_other 0.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.353 r_dihedral_angle_3_deg 15.665 r_dihedral_angle_4_deg 13.79 r_dihedral_angle_1_deg 5.623 r_long_range_B_refined 2.64 r_long_range_B_other 2.64 r_mcangle_it 1.528 r_mcangle_other 1.528 r_angle_refined_deg 1.016 r_scangle_other 0.898 r_mcbond_it 0.821 r_mcbond_other 0.821 r_angle_other_deg 0.703 r_scbond_it 0.447 r_scbond_other 0.445 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8621 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 59
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement DENZO data reduction HKL-2000 data scaling REFMAC phasing