1XVT | pdb_00001xvt

Crystal Structure of Native CaiB 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, 0.1 M Tris-Cl (pH 7.0), VAPOR DIFFUSION, temperature 21K
Crystal Properties
Matthews coefficientSolvent content
3.5965.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.76α = 90
b = 87.76β = 90
c = 164.45γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-04-16MSINGLE 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
12.341.10.05426.75.52932828766
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)
12.32.39990.5674.85.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1XK62.341.12932827309145798.080.198780.196740.20.237130.24RANDOM52.586
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.157
r_dihedral_angle_4_deg15.911
r_dihedral_angle_3_deg15.557
r_dihedral_angle_1_deg5.235
r_scangle_it2.519
r_scbond_it1.681
r_angle_refined_deg1.21
r_mcangle_it0.881
r_mcbond_it0.648
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.157
r_dihedral_angle_4_deg15.911
r_dihedral_angle_3_deg15.557
r_dihedral_angle_1_deg5.235
r_scangle_it2.519
r_scbond_it1.681
r_angle_refined_deg1.21
r_mcangle_it0.881
r_mcbond_it0.648
r_nbtor_refined0.302
r_nbd_refined0.193
r_symmetry_vdw_refined0.181
r_symmetry_hbond_refined0.136
r_xyhbond_nbd_refined0.104
r_chiral_restr0.08
r_bond_refined_d0.01
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 Atoms3028
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms48

Software

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