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Crystal structure of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP), residues 241-576(C363S), form III
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; crystals were dehydrated in 30% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl,pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.29 46.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.863 α = 86.55 b = 83.863 β = 89.55 c = 83.604 γ = 89.38
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 1.5 83.8 80.5 0.055 15.3 2.6 220438 176659 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 1.5 1.5 83.1 0.29 2.4 1.4
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: 3V0D 1.6 83.71 172685 138269 7438 80.07 0.25809 0.25592 0.2561 0.29839 0.298 RANDOM 24.766
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] -1.96 0.42 0.34 0.59 -0.15 1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.908 r_dihedral_angle_4_deg 14.698 r_dihedral_angle_3_deg 13.28 r_dihedral_angle_1_deg 5.286 r_scangle_it 1.268 r_angle_refined_deg 0.956 r_scbond_it 0.806 r_mcangle_it 0.68 r_mcbond_it 0.378 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.908 r_dihedral_angle_4_deg 14.698 r_dihedral_angle_3_deg 13.28 r_dihedral_angle_1_deg 5.286 r_scangle_it 1.268 r_angle_refined_deg 0.956 r_scbond_it 0.806 r_mcangle_it 0.68 r_mcbond_it 0.378 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10548 Nucleic Acid Atoms Solvent Atoms 1169 Heterogen Atoms 45
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling