2AIJ

Formylglycine generating enzyme C336S mutant covalently bound to substrate peptide CTPSR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y1EPDB entry 1Y1E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293PEG 4000, Calcium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.64α = 90
b = 109.592β = 90
c = 43.456γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2005-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.553097.50.03341.24.34260316.43
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.6189.30.1815.63.2

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 1Y1E1.5524.540491206397.430.146010.144420.17777RANDOM18.218
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]
0.140.44-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.023
r_dihedral_angle_4_deg15.761
r_dihedral_angle_3_deg12.418
r_dihedral_angle_1_deg6.432
r_scangle_it2.895
r_scbond_it1.932
r_angle_refined_deg1.408
r_mcangle_it1.374
r_mcbond_it0.906
r_angle_other_deg0.843
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.023
r_dihedral_angle_4_deg15.761
r_dihedral_angle_3_deg12.418
r_dihedral_angle_1_deg6.432
r_scangle_it2.895
r_scbond_it1.932
r_angle_refined_deg1.408
r_mcangle_it1.374
r_mcbond_it0.906
r_angle_other_deg0.843
r_mcbond_other0.231
r_nbd_refined0.217
r_symmetry_vdw_other0.205
r_nbd_other0.204
r_symmetry_hbond_refined0.192
r_nbtor_refined0.188
r_xyhbond_nbd_refined0.167
r_symmetry_vdw_refined0.167
r_chiral_restr0.09
r_nbtor_other0.085
r_metal_ion_refined0.083
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2214
Nucleic Acid Atoms
Solvent Atoms531
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling