4R3W

Crystal Structure Analysis of the 1,2,3-tricarboxylate benzoic acid bound to sp-ASADH-2'5'-ADP complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PWK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529515-22% PEG, 0.1 M Na acetate, 0.1 M MES (pH 6.5), 10 mM TCEP, 3% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3146.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.964α = 90
b = 98.444β = 102.43
c = 64.263γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDdouble crystal monochromator and K-B pair of biomorph mirrors2012-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033APS23-ID-D

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
11.950870.07412.72.7554004934113
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)
11.91.970.3012.82.2

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3PWK1.9162.765670046838249086.630.1880.185870.22892RANDOM37.345
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]
0.470.822.64-3.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.293
r_dihedral_angle_4_deg17.918
r_dihedral_angle_3_deg13.729
r_dihedral_angle_1_deg6.115
r_long_range_B_refined4.954
r_long_range_B_other4.919
r_scangle_other3.669
r_mcangle_it2.761
r_mcangle_other2.724
r_scbond_other2.325
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.293
r_dihedral_angle_4_deg17.918
r_dihedral_angle_3_deg13.729
r_dihedral_angle_1_deg6.115
r_long_range_B_refined4.954
r_long_range_B_other4.919
r_scangle_other3.669
r_mcangle_it2.761
r_mcangle_other2.724
r_scbond_other2.325
r_scbond_it2.32
r_mcbond_it1.833
r_mcbond_other1.832
r_angle_refined_deg1.369
r_angle_other_deg0.76
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5366
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms104

Software

Software
Software NamePurpose
Blue-raydata collection
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling