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Crystal structure of the phosphatase SC4828 with the non-hydrolyzable nucleotide GPCP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CBT PDB entry 3CBT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.1 295 0.2 M CaCl2, 20% PEG 3350, 1 mM GPCP. Cryoprotected in N-paratone oil, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.29 46.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.941 α = 90 b = 79.706 β = 90 c = 82.507 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 IMAGE PLATE RIGAKU RAXIS IV Osmic mirrors 2007-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 1.65 50 97.5 0.033 46.02 6.1 29402 29402 24.2
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 1.65 1.71 80.5 0.256 6.29 3.3 2374
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 3CBT 1.65 25.74 27850 1491 97.5 0.17853 0.17741 0.1736 0.19911 0.1937 RANDOM 24.26
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.523 r_dihedral_angle_4_deg 19.245 r_dihedral_angle_3_deg 14.686 r_dihedral_angle_1_deg 5.844 r_scangle_it 3.409 r_scbond_it 2.159 r_angle_refined_deg 1.505 r_mcangle_it 1.351 r_mcbond_it 0.815 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.523 r_dihedral_angle_4_deg 19.245 r_dihedral_angle_3_deg 14.686 r_dihedral_angle_1_deg 5.844 r_scangle_it 3.409 r_scbond_it 2.159 r_angle_refined_deg 1.505 r_mcangle_it 1.351 r_mcbond_it 0.815 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.151 r_symmetry_metal_ion_refined 0.147 r_symmetry_hbond_refined 0.114 r_chiral_restr 0.104 r_metal_ion_refined 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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_other r_symmetry_vdw_other r_symmetry_hbond_other 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 1714 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 39
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling