2FFB

The crystal structure of the HlyB-NBD E631Q mutant in complex with ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MT0pdb entry 1MT0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8277100 mM Tris, 16% PEG 6000, 5% MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0840.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 178.568α = 90
b = 34.748β = 97.97
c = 37.518γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.05MPG/DESY, HAMBURGBW6

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
11.92094.10.049163702.3
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)
11.91.9594.10.2772.316370

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1MT01.9202.31637087694.10.204030.201610.25023RANDOM37.036
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]
-1.79-3.29-1.011.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.484
r_scangle_it5.377
r_scbond_it3.214
r_mcangle_it2.95
r_mcbond_it1.633
r_angle_refined_deg1.414
r_angle_other_deg0.837
r_symmetry_vdw_other0.249
r_nbd_other0.241
r_nbd_refined0.215
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.484
r_scangle_it5.377
r_scbond_it3.214
r_mcangle_it2.95
r_mcbond_it1.633
r_angle_refined_deg1.414
r_angle_other_deg0.837
r_symmetry_vdw_other0.249
r_nbd_other0.241
r_nbd_refined0.215
r_symmetry_vdw_refined0.199
r_symmetry_hbond_refined0.18
r_xyhbond_nbd_refined0.151
r_nbtor_other0.084
r_chiral_restr0.081
r_bond_other_d0.014
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1912
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing