1XVU

Crystal Structure of CaiB mutant D169A in complex with Coenzyme A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XK6PDB ENTRY 1XK6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72941.35M Sodium citrate, 0.1M Tris-Cl (pH 7.0), VAPOR DIFFUSION, temperature 21K
Crystal Properties
Matthews coefficientSolvent content
3.665.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.838α = 90
b = 86.838β = 90
c = 164.057γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

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
12.4500.06118.37.12531124976
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)
12.42.4999.80.4125.97.5

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1XK62.443.442531123521126597.930.200270.197940.24402RANDOM50.816
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]
0.020.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.323
r_dihedral_angle_3_deg17.168
r_dihedral_angle_4_deg16.974
r_dihedral_angle_1_deg6.027
r_scangle_it2.441
r_scbond_it1.528
r_angle_refined_deg1.371
r_mcangle_it0.892
r_mcbond_it0.509
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.323
r_dihedral_angle_3_deg17.168
r_dihedral_angle_4_deg16.974
r_dihedral_angle_1_deg6.027
r_scangle_it2.441
r_scbond_it1.528
r_angle_refined_deg1.371
r_mcangle_it0.892
r_mcbond_it0.509
r_nbtor_refined0.309
r_nbd_refined0.208
r_symmetry_vdw_refined0.189
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.132
r_chiral_restr0.083
r_bond_refined_d0.013
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3024
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing