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Structure of Protein serine/threonine phosphatase from Saccharomyces cerevisiae with similarity to human phosphatase PP5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WAO PDB entry 1WAO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 0.1 M Hepes 7.5, 0.2 M NaCl, 25% PEG3350 plus 0.015 mg/ml V8 protease. Cryoprotected with Paratone-N oil, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.04 39.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.194 α = 90 b = 47.194 β = 90 c = 237.096 γ = 120
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 315 mirrors 2008-12-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97926 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 40.29 97.9 0.077 29.286 5.5 26308 25761 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 82.9 0.301 3.5 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1WAO 2.3 40.29 24379 1283 97.85 0.19244 0.18993 0.1899 0.23994 0.237 RANDOM 52.813
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.18 r_dihedral_angle_4_deg 20.051 r_dihedral_angle_3_deg 17.901 r_dihedral_angle_1_deg 6.969 r_scangle_it 3.036 r_scbond_it 2.109 r_angle_refined_deg 1.547 r_mcangle_it 1.117 r_mcbond_it 0.603 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.18 r_dihedral_angle_4_deg 20.051 r_dihedral_angle_3_deg 17.901 r_dihedral_angle_1_deg 6.969 r_scangle_it 3.036 r_scbond_it 2.109 r_angle_refined_deg 1.547 r_mcangle_it 1.117 r_mcbond_it 0.603 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.11 r_symmetry_hbond_refined 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5045 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 24
Software Software Software Name Purpose SBC-Collect data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-2000 data scaling