2VTZ

Biosynthetic thiolase from Z. ramigera. Complex of the C89A mutant with coenzyme A.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15pH 5
Crystal Properties
Matthews coefficientSolvent content
2.957.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.22α = 90
b = 79.57β = 92.1
c = 148.92γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
12.32097.20.0715.63.587692-3
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)
12.32.486.10.274.82.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1M3Z2.32080970426297.370.224070.222060.26245RANDOM36.916
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]
-1.4-0.61-1.472.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.456
r_dihedral_angle_4_deg16.469
r_dihedral_angle_3_deg14.23
r_dihedral_angle_1_deg5.565
r_scangle_it1.815
r_scbond_it1.267
r_angle_refined_deg1.127
r_mcangle_it0.821
r_angle_other_deg0.778
r_mcbond_it0.658
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.456
r_dihedral_angle_4_deg16.469
r_dihedral_angle_3_deg14.23
r_dihedral_angle_1_deg5.565
r_scangle_it1.815
r_scbond_it1.267
r_angle_refined_deg1.127
r_mcangle_it0.821
r_angle_other_deg0.778
r_mcbond_it0.658
r_symmetry_vdw_other0.256
r_symmetry_vdw_refined0.255
r_symmetry_hbond_refined0.209
r_nbd_refined0.194
r_xyhbond_nbd_refined0.182
r_nbd_other0.178
r_nbtor_refined0.164
r_nbtor_other0.082
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11248
Nucleic Acid Atoms
Solvent Atoms805
Heterogen Atoms222

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling