4MAV

Crystal structure of signaling protein SPB-40 complexed with 5-hydroxymethyl oxalanetriol at 2.80 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O9O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829825mM Tris, 50mM NaCl, 20% ethanol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6553.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.809α = 90
b = 66.943β = 90
c = 106.54γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMIRROR2013-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.79501000.10816.61128011280
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.851000.464.1

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2O9O2.7941.72112801070353599.560.182410.182390.181920.23391RANDOM32.923
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]
-0.74-1.171.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.309
r_dihedral_angle_3_deg21.274
r_dihedral_angle_4_deg20.704
r_long_range_B_refined7.658
r_long_range_B_other7.657
r_dihedral_angle_1_deg7
r_scangle_other4.146
r_mcangle_other3.828
r_mcangle_it3.824
r_scbond_it2.464
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.309
r_dihedral_angle_3_deg21.274
r_dihedral_angle_4_deg20.704
r_long_range_B_refined7.658
r_long_range_B_other7.657
r_dihedral_angle_1_deg7
r_scangle_other4.146
r_mcangle_other3.828
r_mcangle_it3.824
r_scbond_it2.464
r_scbond_other2.463
r_mcbond_it2.227
r_mcbond_other2.216
r_angle_refined_deg1.861
r_angle_other_deg0.849
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2894
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms30

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling