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X-ray crystal structure of Protein Phosphatase-1 with the marine toxin motuporin bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JK7 PDB ID 1JK7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 273 2.3 M lithium sulfate, Tris-HCl (100 mM, pH 8.0), polyethylene glycol 400 (2%), beta-mercaptoethanol (10 mM), VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.18 43.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.955 α = 90 b = 100.955 β = 90 c = 63.485 γ = 90
Symmetry Space Group P 42 21 2
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 ADSC QUANTUM 4 mirrors 2003-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.0 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 45.13 99.9 0.065 0.065 7.1 3.7 19722 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.21 100 100 0.293 0.293 2.5 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 ID 1JK7 2.1 31.75 3 19682 1008 99.92 0.223 0.223 0.221 0.222 0.264 0.266 RANDOM 26.439
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.609 r_dihedral_angle_4_deg 15.697 r_dihedral_angle_3_deg 15.034 r_dihedral_angle_1_deg 6.782 r_scangle_it 2.943 r_scbond_it 2.116 r_angle_refined_deg 1.838 r_mcangle_it 1.486 r_mcbond_it 0.926 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.609 r_dihedral_angle_4_deg 15.697 r_dihedral_angle_3_deg 15.034 r_dihedral_angle_1_deg 6.782 r_scangle_it 2.943 r_scbond_it 2.116 r_angle_refined_deg 1.838 r_mcangle_it 1.486 r_mcbond_it 0.926 r_nbtor_refined 0.3 r_xyhbond_nbd_refined 0.169 r_symmetry_vdw_refined 0.169 r_nbd_refined 0.155 r_chiral_restr 0.117 r_symmetry_hbond_refined 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2405 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 16
Software Software Software Name Purpose SCALA data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling