2VJO

Formyl-CoA transferase mutant variant Q17A with aspartyl-CoA thioester intermediates and oxalate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.8656.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.593α = 90
b = 153.593β = 90
c = 98.055γ = 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
12.241.399.50.129.33.2574622
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)
12.22.321000.571.93.1

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 1P5H2.23054545289499.40.2080.2060.248RANDOM32.86
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]
0.210.21-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.34
r_dihedral_angle_4_deg18.826
r_dihedral_angle_3_deg15.102
r_dihedral_angle_1_deg5.735
r_scangle_it1.557
r_angle_refined_deg1.153
r_scbond_it1.007
r_mcangle_it0.926
r_mcbond_it0.531
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.34
r_dihedral_angle_4_deg18.826
r_dihedral_angle_3_deg15.102
r_dihedral_angle_1_deg5.735
r_scangle_it1.557
r_angle_refined_deg1.153
r_scbond_it1.007
r_mcangle_it0.926
r_mcbond_it0.531
r_nbtor_refined0.295
r_nbd_refined0.175
r_symmetry_vdw_refined0.169
r_symmetry_hbond_refined0.146
r_xyhbond_nbd_refined0.14
r_chiral_restr0.095
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms6616
Nucleic Acid Atoms
Solvent Atoms440
Heterogen Atoms119

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing