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Crystal Structure of Protein Phosphatase-1 Bound to the natural toxin Nodularin-R
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FJM PDB entry 1FJM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 298 20% PEG 3350 and 0.2 M NaI, pH 7.0, under parafin oil, temperature 298K, Microbatch
Crystal Properties Matthews coefficient Solvent content 2.41 49.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.354 α = 90 b = 77.274 β = 90 c = 132.444 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC QUANTUM 210 Oxford Danfysik toroidal focusing mirror. 2008-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.000 NSLS X6A
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 1.63 50 99.3 0.072 7.2 83995 83444 3 1
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 1.63 1.69 93.5 0.51 2.3 4.1 7804
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 1FJM 1.63 26.57 83995 79699 4185 99.73 0.144 0.143 0.1519 0.169 0.1778 RANDOM 12.9
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] -0.38 0.15 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.809 r_dihedral_angle_4_deg 16.732 r_dihedral_angle_3_deg 10.805 r_dihedral_angle_1_deg 6.607 r_scangle_it 4.418 r_scbond_it 3.066 r_mcangle_it 1.954 r_angle_refined_deg 1.374 r_mcbond_it 1.23 r_angle_other_deg 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.809 r_dihedral_angle_4_deg 16.732 r_dihedral_angle_3_deg 10.805 r_dihedral_angle_1_deg 6.607 r_scangle_it 4.418 r_scbond_it 3.066 r_mcangle_it 1.954 r_angle_refined_deg 1.374 r_mcbond_it 1.23 r_angle_other_deg 0.93 r_mcbond_other 0.318 r_symmetry_vdw_other 0.228 r_nbd_refined 0.219 r_nbd_other 0.203 r_symmetry_hbond_refined 0.195 r_symmetry_vdw_refined 0.183 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.163 r_nbtor_other 0.083 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4753 Nucleic Acid Atoms Solvent Atoms 682 Heterogen Atoms 40
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection