2AII

wild-type Formylglycine generating enzyme reacted with iodoacetamide


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
2.2745.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.058α = 90
b = 109.788β = 90
c = 43.461γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2005-01-28MSINGLE 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
11.545098.50.04541.56.64415514.19
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)
11.541.685.50.2294.93.7

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 1Y1E1.5443.4841989211699.030.151630.15040.17598RANDOM11.798
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]
0.150.22-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.195
r_dihedral_angle_4_deg16.184
r_dihedral_angle_3_deg12.429
r_dihedral_angle_1_deg6.458
r_scangle_it2.688
r_scbond_it1.766
r_angle_refined_deg1.306
r_mcangle_it1.238
r_angle_other_deg0.843
r_mcbond_it0.774
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.195
r_dihedral_angle_4_deg16.184
r_dihedral_angle_3_deg12.429
r_dihedral_angle_1_deg6.458
r_scangle_it2.688
r_scbond_it1.766
r_angle_refined_deg1.306
r_mcangle_it1.238
r_angle_other_deg0.843
r_mcbond_it0.774
r_nbd_refined0.229
r_nbd_other0.202
r_symmetry_vdw_other0.201
r_symmetry_hbond_refined0.199
r_nbtor_refined0.189
r_symmetry_vdw_refined0.18
r_mcbond_other0.178
r_xyhbond_nbd_refined0.173
r_chiral_restr0.089
r_nbtor_other0.081
r_metal_ion_refined0.027
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms2173
Nucleic Acid Atoms
Solvent Atoms523
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling