3SLB

Crystal structure of BA2930 in complex with AcCoA and cytosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KZLPDB entry 3KZL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M HEPES-Na, 0.18M MgCl2, 15% w/v PEG3350, 2% w/v CHAPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2645.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.473α = 90
b = 110.63β = 112.24
c = 73.78γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDberyllium lenses2010-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9786APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
125097.20.0940.09415.737063470634-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.03990.4180.4182.633593

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 3KZL223.996690666906354696.980.177120.177120.174310.22957RANDOM27.617
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]
-0.17-0.15-0.140.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.465
r_dihedral_angle_4_deg17.888
r_dihedral_angle_3_deg14.979
r_dihedral_angle_1_deg6.149
r_scangle_it3.581
r_scbond_it2.369
r_angle_refined_deg1.48
r_mcangle_it1.273
r_angle_other_deg0.962
r_mcbond_it0.685
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.465
r_dihedral_angle_4_deg17.888
r_dihedral_angle_3_deg14.979
r_dihedral_angle_1_deg6.149
r_scangle_it3.581
r_scbond_it2.369
r_angle_refined_deg1.48
r_mcangle_it1.273
r_angle_other_deg0.962
r_mcbond_it0.685
r_mcbond_other0.177
r_chiral_restr0.084
r_bond_refined_d0.014
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.001
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 Atoms8242
Nucleic Acid Atoms
Solvent Atoms670
Heterogen Atoms297

Software

Software
Software NamePurpose
MD2data collection
HKL-3000phasing
MOLREPphasing
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling