2VJK

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.7154

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.906α = 90
b = 151.906β = 90
c = 99.504γ = 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
1256.0899.20.1110.13.6756552
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)
122.1197.20.32.42.8

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 1P5H1.973074942391098.80.1750.1730.214RANDOM23.59
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]
0.120.12-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.394
r_dihedral_angle_4_deg16.215
r_dihedral_angle_3_deg13.479
r_dihedral_angle_1_deg5.698
r_scangle_it1.89
r_mcangle_it1.601
r_mcbond_it1.417
r_scbond_it1.337
r_angle_refined_deg1.116
r_angle_other_deg0.886
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.394
r_dihedral_angle_4_deg16.215
r_dihedral_angle_3_deg13.479
r_dihedral_angle_1_deg5.698
r_scangle_it1.89
r_mcangle_it1.601
r_mcbond_it1.417
r_scbond_it1.337
r_angle_refined_deg1.116
r_angle_other_deg0.886
r_nbd_refined0.183
r_nbd_other0.182
r_symmetry_vdw_other0.179
r_nbtor_refined0.168
r_symmetry_vdw_refined0.139
r_xyhbond_nbd_refined0.133
r_symmetry_hbond_refined0.123
r_nbtor_other0.082
r_chiral_restr0.072
r_bond_refined_d0.008
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 Atoms787
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing