3V0H

Crystal structure of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP), residues 241-576(C363S), complexed with D-MYO-inositol-1,4,5-triphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3V0DPDB: 3V0D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP827717.5-22.5% PEG 2000, 0.1 M ammonium dihydrophosphate, 0.1 M Tris-HCl, pH 8.0; complex was made by soaking method, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2946.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.665α = 90
b = 79.852β = 92.44
c = 87.927γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rDouble Crystal Si(111)2010-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1158ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.858999.90.11117.27.4599005984022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9299.60.663.47.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB: 3V0D1.8587.855672856716302199.90.182790.180680.22229RANDOM22.942
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]
-0.87-0.090.650.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.117
r_dihedral_angle_4_deg16.792
r_dihedral_angle_3_deg14.028
r_dihedral_angle_1_deg5.709
r_scangle_it2.488
r_scbond_it1.496
r_angle_refined_deg1.224
r_mcangle_it1.054
r_mcbond_it0.538
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.117
r_dihedral_angle_4_deg16.792
r_dihedral_angle_3_deg14.028
r_dihedral_angle_1_deg5.709
r_scangle_it2.488
r_scbond_it1.496
r_angle_refined_deg1.224
r_mcangle_it1.054
r_mcbond_it0.538
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5266
Nucleic Acid Atoms
Solvent Atoms675
Heterogen Atoms96

Software

Software
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling