2BUE

Structure of AAC(6')-Ib in complex with Ribostamycin and Coenzyme A.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V0CPDB ENTRY 1V0C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.75PROTEIN (10MG/ML, 20 MM TRIS PH 7.5, 20 MM NACL, 3 MM ACCOA) PRECIPITANT (20% PEG3350, 200 MM CALCIUM ACETATE, 100 MM NACACODYLATE PH 6.75) VAPOR DIFFUSION UNDER OIL
Crystal Properties
Matthews coefficientSolvent content
2.4655.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.475α = 90
b = 57.475β = 90
c = 148.305γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU-MSC RAXIS-IV2006-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
11.724.29970.0433.27.427341
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)
11.71.7984.70.216.96

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1V0C1.7149.0725956138296.40.1840.1820.211RANDOM17.58
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]
0.120.12-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.549
r_dihedral_angle_4_deg15.64
r_dihedral_angle_3_deg12.183
r_dihedral_angle_1_deg5.248
r_scangle_it3.461
r_scbond_it2.15
r_mcangle_it1.482
r_angle_refined_deg1.335
r_mcbond_it0.928
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.549
r_dihedral_angle_4_deg15.64
r_dihedral_angle_3_deg12.183
r_dihedral_angle_1_deg5.248
r_scangle_it3.461
r_scbond_it2.15
r_mcangle_it1.482
r_angle_refined_deg1.335
r_mcbond_it0.928
r_nbtor_refined0.305
r_symmetry_hbond_refined0.228
r_symmetry_vdw_refined0.202
r_nbd_refined0.195
r_xyhbond_nbd_refined0.138
r_chiral_restr0.088
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1404
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling