4Y4M

Thiazole synthase Thi4 from Methanocaldococcus jannaschii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RP0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION9.52951.05 M Potassium/sodium tartrate, 0.1 M CHES/ Sodium hydroxide pH 9.5, 0.2 M Lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.7660.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.76α = 90
b = 180.76β = 90
c = 73.328γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9791APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.74099.30.0720.07213.33.572800

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 REPLACEMENTTHROUGHOUT1RP02.714068627364699.010.178410.177080.20311RANDOM54.853
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]
0.810.40.81-2.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.608
r_dihedral_angle_4_deg20.202
r_dihedral_angle_3_deg16.322
r_long_range_B_refined9.971
r_long_range_B_other9.971
r_scangle_other6.613
r_dihedral_angle_1_deg6.054
r_mcangle_it4.525
r_mcangle_other4.525
r_scbond_it4.143
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.608
r_dihedral_angle_4_deg20.202
r_dihedral_angle_3_deg16.322
r_long_range_B_refined9.971
r_long_range_B_other9.971
r_scangle_other6.613
r_dihedral_angle_1_deg6.054
r_mcangle_it4.525
r_mcangle_other4.525
r_scbond_it4.143
r_scbond_other4.143
r_angle_other_deg3.659
r_mcbond_it2.963
r_mcbond_other2.962
r_angle_refined_deg1.361
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_gen_planes_other0.004
r_bond_other_d
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15270
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms353

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing