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Crystal structure of Pten-like domain of Ci-VSP (236-576)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D5R PDB ENTRY 1D5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 2.1M AMMONIUM SULFATE, 0.1M TRIS, 0.5M SODIUM FLUORIDE, 1.0M SODIUM MALONATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 50.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.556 α = 90 b = 177.439 β = 90 c = 50.936 γ = 90
Symmetry Space Group P 21 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 Bruker DIP-6040 HORIZONTAL FOCUSING MIRROR 2008-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.99 50 99.6 0.086 19.621 4.8 81701 -3 23.9
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 1.99 2.07 99.6 0.494 4.6
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 1D5R 1.99 44.17 81627 4093 98.8 0.181 0.179 0.179 0.223 0.2249 RANDOM 28.22
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] -0.67 1.89 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.861 r_dihedral_angle_4_deg 21.618 r_dihedral_angle_3_deg 15.342 r_dihedral_angle_1_deg 7.34 r_scangle_it 5.569 r_scbond_it 3.482 r_mcangle_it 2.209 r_angle_refined_deg 1.935 r_mcbond_it 1.287 r_chiral_restr 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.861 r_dihedral_angle_4_deg 21.618 r_dihedral_angle_3_deg 15.342 r_dihedral_angle_1_deg 7.34 r_scangle_it 5.569 r_scbond_it 3.482 r_mcangle_it 2.209 r_angle_refined_deg 1.935 r_mcbond_it 1.287 r_chiral_restr 0.154 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 7408 Nucleic Acid Atoms Solvent Atoms 535 Heterogen Atoms 56
Software Software Software Name Purpose BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling