3VB1

Crystal Structure of Anopholes gambiae odorant binding protein 20 in open state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3V2LPDB ENTRY 3V2L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.572761.9 M ammonium sulfate, 0.2 M potassium sodium tartrate, 0.1 M sodium citrate, pH 5.57, VAPOR DIFFUSION, HANGING DROP, temperature 276K
Crystal Properties
Matthews coefficientSolvent content
2.1843.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.923α = 90
b = 36.463β = 90
c = 92.091γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12007-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.0ALS4.2.2

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
11.9533.999.70.04615.84.419029902922
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)
11.952.021000.1985.54.53893

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3V2L232.658348834882898.90.23480.23480.23060.2711RANDOM38.4144
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]
-2.733.58-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.275
r_dihedral_angle_3_deg17.288
r_dihedral_angle_4_deg16.348
r_dihedral_angle_1_deg6.048
r_scangle_it4.183
r_scbond_it2.999
r_mcangle_it1.568
r_angle_refined_deg1.383
r_mcbond_it0.967
r_angle_other_deg0.898
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.275
r_dihedral_angle_3_deg17.288
r_dihedral_angle_4_deg16.348
r_dihedral_angle_1_deg6.048
r_scangle_it4.183
r_scbond_it2.999
r_mcangle_it1.568
r_angle_refined_deg1.383
r_mcbond_it0.967
r_angle_other_deg0.898
r_mcbond_other0.319
r_chiral_restr0.082
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms920
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms4

Software

Software
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
JBluIce-EPICSdata collection
Blu-Icedata collection