3V0J

Crystal structure of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP), residues 241-576(C363S), Deletion of 401-405


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, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1342.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.562α = 90
b = 76.804β = 92.73
c = 84.007γ = 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)2010-07-29MSINGLE 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
11.721001000.11614.4689186890322
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)
11.721.781000.7423.7

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: 3V0D1.7283.916476364627344199.790.187120.185220.22239RANDOM26.27
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]
-1.53-0.312.86-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.042
r_dihedral_angle_4_deg14.264
r_dihedral_angle_3_deg13.99
r_dihedral_angle_1_deg5.851
r_scangle_it2.54
r_scbond_it1.536
r_angle_refined_deg1.107
r_mcangle_it1.091
r_mcbond_it0.57
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.042
r_dihedral_angle_4_deg14.264
r_dihedral_angle_3_deg13.99
r_dihedral_angle_1_deg5.851
r_scangle_it2.54
r_scbond_it1.536
r_angle_refined_deg1.107
r_mcangle_it1.091
r_mcbond_it0.57
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5156
Nucleic Acid Atoms
Solvent Atoms506
Heterogen Atoms10

Software

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