☰ Navigation Tabs
Crystal structure of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP), residues 241-576(C363S), form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V0D PDB: 3V0D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 17.5-22.5% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl,pH 8.0; crystal were soaked in 30% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl, pH 8.0 to remove phosphate by serial dilution, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.19 43.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.746 α = 90 b = 80.375 β = 93.12 c = 83.637 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 ADSC QUANTUM 315r Double Crystal Si(111) 2010-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1158 ALS 8.3.1
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 1.3 84 94.1 0.084 26.3 12.5 163916 153889 2 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 1.3 1.33 90.1 0.584 3.5 7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB: 3V0D 1.3 83.51 155675 146117 7732 93.86 0.14156 0.13984 0.17502 0.1867 RANDOM 22.827
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] -0.55 -0.09 0.45 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.075 r_dihedral_angle_4_deg 16.186 r_dihedral_angle_3_deg 12.99 r_dihedral_angle_1_deg 6.247 r_scangle_it 4.305 r_scbond_it 2.79 r_mcangle_it 2.158 r_angle_refined_deg 1.354 r_mcbond_it 1.302 r_rigid_bond_restr 1.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.075 r_dihedral_angle_4_deg 16.186 r_dihedral_angle_3_deg 12.99 r_dihedral_angle_1_deg 6.247 r_scangle_it 4.305 r_scbond_it 2.79 r_mcangle_it 2.158 r_angle_refined_deg 1.354 r_mcbond_it 1.302 r_rigid_bond_restr 1.205 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5259 Nucleic Acid Atoms Solvent Atoms 870 Heterogen Atoms 10
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling