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Crystal structure of the serine/threonine phosphatase domain of human PPM1B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A6Q PDB entry 1A6Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 294 100mM Hepes pH 7.5, 20% PEG 4000, 10% Isopropanol, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.09 41.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.399 α = 90 b = 92.315 β = 90 c = 118.713 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 100 CCD MAR CCD 165 mm 2007-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-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 1.816 72.932 93.8 0.184 0.184 8.3 5.4 49509 49509 17.4
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) 1.816 1.91 84.5 0.842 0.842 1.5 4.8 6430
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 1A6Q 1.816 20 49432 49432 2523 93.8 0.189 0.186 0.1892 0.246 0.2469 RANDOM 22.186
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] -0.71 1.33 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.085 r_dihedral_angle_4_deg 19.126 r_dihedral_angle_3_deg 14.57 r_dihedral_angle_1_deg 5.964 r_scangle_it 4.039 r_scbond_it 2.689 r_mcangle_it 1.578 r_angle_refined_deg 1.503 r_mcbond_it 1.039 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.085 r_dihedral_angle_4_deg 19.126 r_dihedral_angle_3_deg 14.57 r_dihedral_angle_1_deg 5.964 r_scangle_it 4.039 r_scbond_it 2.689 r_mcangle_it 1.578 r_angle_refined_deg 1.503 r_mcbond_it 1.039 r_nbtor_refined 0.305 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.2 r_symmetry_vdw_refined 0.196 r_symmetry_hbond_refined 0.168 r_chiral_restr 0.108 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4438 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 2
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling AMoRE phasing