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Crystal structure of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP), residues 241-576(C363S)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D5R
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, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.37 48.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.967 α = 90 b = 85.706 β = 90.96 c = 84.327 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) 2009-12-04 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 1.1 86 99.6 0.054 4.2 292576 291443 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 1.1 1.12 96.9 0.475 2.2 2.9
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 entry1D5R 1.1 84.32 277795 276406 14723 99.5 0.14095 0.13988 0.1455 0.16073 0.1663 RANDOM 23.618
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] -0.71 -0.65 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.743 r_dihedral_angle_4_deg 17.104 r_dihedral_angle_3_deg 12.874 r_dihedral_angle_1_deg 6.287 r_scangle_it 4.534 r_scbond_it 2.953 r_mcangle_it 2.35 r_angle_refined_deg 1.472 r_mcbond_it 1.469 r_rigid_bond_restr 1.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.743 r_dihedral_angle_4_deg 17.104 r_dihedral_angle_3_deg 12.874 r_dihedral_angle_1_deg 6.287 r_scangle_it 4.534 r_scbond_it 2.953 r_mcangle_it 2.35 r_angle_refined_deg 1.472 r_mcbond_it 1.469 r_rigid_bond_restr 1.348 r_chiral_restr 0.103 r_bond_refined_d 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5245 Nucleic Acid Atoms Solvent Atoms 975 Heterogen Atoms 20
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling