3K31

Crystal structure of eonyl-(acyl-carrier-protein) reductase from anaplasma phagocytophilum in complex with nad at 1.9a resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3K2Enative structure, pdb entry 3k2e

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8290JCSG+ SCREEN CONDITION E11: 100MM IMIDAZOLE PH 80, 10% PEG 8000; ANPHA.00817.A AT 23MG/ML WITH 1MM NAD, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.2545.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.78α = 90
b = 89.73β = 90
c = 79.11γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252009-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97351CLSI08ID-1

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
11.85099.80.06820.747.25396953869-327.36
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)
11.81.8599.90.4915.63924

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTnative structure, pdb entry 3k2e1.819.785386953867270999.90.150.150.1480.175RANDOM16.54
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]
0.370.24-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.356
r_dihedral_angle_4_deg14.964
r_dihedral_angle_3_deg11.911
r_dihedral_angle_1_deg5.474
r_scangle_it4.593
r_scbond_it2.776
r_mcangle_it1.771
r_angle_refined_deg1.523
r_angle_other_deg1.003
r_mcbond_it0.969
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.356
r_dihedral_angle_4_deg14.964
r_dihedral_angle_3_deg11.911
r_dihedral_angle_1_deg5.474
r_scangle_it4.593
r_scbond_it2.776
r_mcangle_it1.771
r_angle_refined_deg1.523
r_angle_other_deg1.003
r_mcbond_it0.969
r_mcbond_other0.273
r_chiral_restr0.092
r_bond_refined_d0.016
r_gen_planes_refined0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3825
Nucleic Acid Atoms
Solvent Atoms364
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling