2VJM

Formyl-CoA transferase with aspartyl-formyl anhydide intermediate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.668α = 90
b = 151.668β = 90
c = 98.947γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-2MAX III911-2

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
11.8744.997.10.0715.94.1895772
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)
11.871.9781.10.364.23.5

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 1P5H1.893085088447399.30.1730.1710.203RANDOM20.01
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]
0.10.1-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.156
r_dihedral_angle_4_deg14.827
r_dihedral_angle_3_deg12.817
r_dihedral_angle_1_deg5.545
r_scangle_it1.882
r_scbond_it1.146
r_angle_refined_deg1.053
r_mcangle_it0.926
r_angle_other_deg0.874
r_mcbond_it0.497
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.156
r_dihedral_angle_4_deg14.827
r_dihedral_angle_3_deg12.817
r_dihedral_angle_1_deg5.545
r_scangle_it1.882
r_scbond_it1.146
r_angle_refined_deg1.053
r_mcangle_it0.926
r_angle_other_deg0.874
r_mcbond_it0.497
r_symmetry_vdw_other0.251
r_nbd_refined0.191
r_nbd_other0.18
r_nbtor_refined0.168
r_symmetry_vdw_refined0.126
r_xyhbond_nbd_refined0.12
r_symmetry_hbond_refined0.09
r_nbtor_other0.08
r_chiral_restr0.06
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 Atoms6627
Nucleic Acid Atoms
Solvent Atoms756
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing