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X-ray Crystal Structure of dihydromicrocystin-LA bound to Protein Phosphatase-1
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%) and beta-mercaptoethanol (10 mM), VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 2.12 42.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.978 α = 90 b = 99.978 β = 90 c = 62.949 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 2.3 100 99.9 0.067 0.067 8.5 7.7 14724 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 2.3 2.42 100 100 0.267 0.267 2.5 7.6 2101
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 2.3 35.36 3 14689 739 99.94 0.214 0.214 0.212 0.21 0.25 0.2497 RANDOM 32.699
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] -0.05 -0.05 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.223 r_dihedral_angle_4_deg 18.294 r_dihedral_angle_3_deg 15.76 r_dihedral_angle_1_deg 7.182 r_scangle_it 3.016 r_scbond_it 2.02 r_mcangle_it 1.63 r_angle_refined_deg 1.574 r_mcbond_it 0.948 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.223 r_dihedral_angle_4_deg 18.294 r_dihedral_angle_3_deg 15.76 r_dihedral_angle_1_deg 7.182 r_scangle_it 3.016 r_scbond_it 2.02 r_mcangle_it 1.63 r_angle_refined_deg 1.574 r_mcbond_it 0.948 r_nbtor_refined 0.302 r_xyhbond_nbd_refined 0.162 r_nbd_refined 0.147 r_symmetry_hbond_refined 0.13 r_symmetry_vdw_refined 0.122 r_chiral_restr 0.106 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2403 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 2
Software Software Software Name Purpose SCALA data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling