3OB6

Structure of AdiC(N101A) in the open-to-out Arg+ bound conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LRBPDB ENTRY 3LRB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529824-28% PEG400, 2mM Cymal-5, 1mM LDAO, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.5465.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.071α = 90
b = 77.204β = 106.79
c = 104.451γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9791ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
133093.36.83.325006246811.51.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
33.1173.42.42.6

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 3LRB3252334923349125592.960.244730.243280.27202RANDOM47.695
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]
-7.01-1.977.67-1.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.67
r_dihedral_angle_3_deg20.656
r_dihedral_angle_4_deg16.245
r_dihedral_angle_1_deg6.665
r_scangle_it1.694
r_angle_refined_deg1.418
r_angle_other_deg1.063
r_scbond_it1.024
r_mcangle_it0.745
r_mcbond_it0.381
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.67
r_dihedral_angle_3_deg20.656
r_dihedral_angle_4_deg16.245
r_dihedral_angle_1_deg6.665
r_scangle_it1.694
r_angle_refined_deg1.418
r_angle_other_deg1.063
r_scbond_it1.024
r_mcangle_it0.745
r_mcbond_it0.381
r_chiral_restr0.094
r_mcbond_other0.07
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6411
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms24

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
DNAdata collection
DENZOdata reduction
SCALEPACKdata scaling