3V0F

Crystal structure of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP), residues 241-576(C363S), form II


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; 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 coefficientSolvent content
2.1943.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.746α = 90
b = 80.375β = 93.12
c = 83.637γ = 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
11.38494.10.08426.312.516391615388922
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)
11.31.3390.10.5843.57

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: 3V0D1.383.51155675146117773293.860.141560.139840.17502RANDOM22.827
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]
-0.55-0.090.450.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.075
r_dihedral_angle_4_deg16.186
r_dihedral_angle_3_deg12.99
r_dihedral_angle_1_deg6.247
r_scangle_it4.305
r_scbond_it2.79
r_mcangle_it2.158
r_angle_refined_deg1.354
r_mcbond_it1.302
r_rigid_bond_restr1.205
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.075
r_dihedral_angle_4_deg16.186
r_dihedral_angle_3_deg12.99
r_dihedral_angle_1_deg6.247
r_scangle_it4.305
r_scbond_it2.79
r_mcangle_it2.158
r_angle_refined_deg1.354
r_mcbond_it1.302
r_rigid_bond_restr1.205
r_chiral_restr0.096
r_bond_refined_d0.01
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5259
Nucleic Acid Atoms
Solvent Atoms870
Heterogen Atoms10

Software

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