3V0E

Crystal structure of Ciona intestinalis voltage sensor-containing phosphatase (Ci-VSP), residues 256-576(C363S)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D5RPDB entry 1D5R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52952.1-2.3 M ammonium sulfate, 0.1 M HEPES, pH 7.0-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3146.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.849α = 90
b = 38.605β = 103.99
c = 89.832γ = 90
Symmetry
Space GroupP 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rDouble Crystal Si(111)2009-10-10MSINGLE 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
11.69097.70.0718.15.8449344375022
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)
11.61.6582.20.6722.44.1

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 entry 1D5R1.6587.174119338746205899.050.178290.17660.20959RANDOM32.126
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]
-1.96-0.633.71-2.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.244
r_dihedral_angle_4_deg14.152
r_dihedral_angle_3_deg12.588
r_dihedral_angle_1_deg5.352
r_scangle_it3.078
r_scbond_it1.934
r_mcangle_it1.799
r_angle_refined_deg1.081
r_rigid_bond_restr1.007
r_mcbond_it0.993
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.244
r_dihedral_angle_4_deg14.152
r_dihedral_angle_3_deg12.588
r_dihedral_angle_1_deg5.352
r_scangle_it3.078
r_scbond_it1.934
r_mcangle_it1.799
r_angle_refined_deg1.081
r_rigid_bond_restr1.007
r_mcbond_it0.993
r_chiral_restr0.08
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2570
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms34

Software

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