9FDD

The crystal structure of full length tetramer CysB from Klebsiella aerogenes in complex with N-acetylserine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AL3c

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529112-17% PEG 8000, 0.2 M sodium tartrate, 0.1 M Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.6453.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 187.436α = 90
b = 187.436β = 90
c = 224.662γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 41998-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.60.87SRSPX9.6

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
12.841.46299.40.0895.95.77241535.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.841.46272368362699.9160.1830.180.245645.469
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]
0.8620.4310.862-2.797
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.357
r_dihedral_angle_6_deg14.245
r_lrange_it9.309
r_lrange_other9.308
r_dihedral_angle_2_deg7.41
r_dihedral_angle_1_deg7.234
r_scangle_it6.563
r_scangle_other6.563
r_mcangle_it6.35
r_mcangle_other6.349
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.357
r_dihedral_angle_6_deg14.245
r_lrange_it9.309
r_lrange_other9.308
r_dihedral_angle_2_deg7.41
r_dihedral_angle_1_deg7.234
r_scangle_it6.563
r_scangle_other6.563
r_mcangle_it6.35
r_mcangle_other6.349
r_scbond_it4.046
r_scbond_other4.046
r_mcbond_it3.98
r_mcbond_other3.98
r_angle_refined_deg1.753
r_angle_other_deg0.587
r_symmetry_nbd_refined0.224
r_nbd_refined0.223
r_symmetry_nbd_other0.207
r_nbd_other0.196
r_symmetry_xyhbond_nbd_refined0.185
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.141
r_symmetry_nbtor_other0.082
r_chiral_restr0.079
r_symmetry_xyhbond_nbd_other0.063
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20288
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
HKL-3000data reduction
Aimlessdata scaling
MOLREPphasing