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Structure of serine/threonine protein phosphatase 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IT6 Partial homology model derived from 1IT6, 1AUJ, 1G5B experimental model PDB 1AUJ Partial homology model derived from 1IT6, 1AUJ, 1G5B experimental model PDB 1G5B Partial homology model derived from 1IT6, 1AUJ, 1G5B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 2-methyl,2,4-pentanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.45 30
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.808 α = 90 b = 80.309 β = 94.25 c = 92.189 γ = 90
Symmetry Space Group P 1 21 1
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 MARRESEARCH 2002-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
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 1.47 40 70 0.064 0.064 8.9 2.9 70964 70964 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.59 13 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 Partial homology model derived from 1IT6, 1AUJ, 1G5B 1.6 40 2 70964 70964 3431 86.48 0.17125 0.17125 0.16929 0.1824 0.20933 0.2214 RANDOM 23.31
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] -0.44 -0.47 1.79 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.799 r_dihedral_angle_3_deg 13.046 r_dihedral_angle_4_deg 12.235 r_dihedral_angle_1_deg 4.445 r_scangle_it 3.546 r_scbond_it 2.652 r_angle_refined_deg 1.553 r_mcangle_it 1.323 r_mcbond_it 1.224 r_angle_other_deg 0.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.799 r_dihedral_angle_3_deg 13.046 r_dihedral_angle_4_deg 12.235 r_dihedral_angle_1_deg 4.445 r_scangle_it 3.546 r_scbond_it 2.652 r_angle_refined_deg 1.553 r_mcangle_it 1.323 r_mcbond_it 1.224 r_angle_other_deg 0.958 r_mcbond_other 0.341 r_symmetry_vdw_other 0.288 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.207 r_nbd_other 0.195 r_symmetry_hbond_refined 0.186 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.133 r_xyhbond_nbd_other 0.09 r_nbtor_other 0.089 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5203 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling MOLREP phasing