2VJL

Formyl-CoA transferase with aspartyl-CoA thioester intermediate derived from formyl-CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P5HPDB ENTRY 1P5H

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.7655

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.765α = 90
b = 151.765β = 90
c = 100.082γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
125698.30.118.73.1752332
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)
122.1194.30.391.82.4

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 1P5H23071459376598.20.1990.1970.242RANDOM25.35
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]
0.070.07-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.239
r_dihedral_angle_4_deg16.811
r_dihedral_angle_3_deg13.3
r_dihedral_angle_1_deg5.677
r_scangle_it1.698
r_mcangle_it1.574
r_mcbond_it1.397
r_scbond_it1.216
r_angle_refined_deg1.075
r_angle_other_deg0.855
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.239
r_dihedral_angle_4_deg16.811
r_dihedral_angle_3_deg13.3
r_dihedral_angle_1_deg5.677
r_scangle_it1.698
r_mcangle_it1.574
r_mcbond_it1.397
r_scbond_it1.216
r_angle_refined_deg1.075
r_angle_other_deg0.855
r_nbd_refined0.179
r_nbd_other0.179
r_symmetry_vdw_refined0.174
r_nbtor_refined0.167
r_xyhbond_nbd_refined0.14
r_symmetry_vdw_other0.126
r_symmetry_hbond_refined0.125
r_nbtor_other0.081
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
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 Atoms6624
Nucleic Acid Atoms
Solvent Atoms694
Heterogen Atoms101

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing