2G9I

Crystal structure of homolog of F420-0:gamma-Glutamyl Ligase from Archaeoglobus fulgidus Reveals a Novel Fold.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529130% PEG 2K MME, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1342.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.386α = 90
b = 100.386β = 90
c = 92.96γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-06-20MSAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9795APS19-ID

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
12.5401000.10940.330.41699216992
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)
12.52.541000.5655.124.1

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAD2.540169361608185599.670.19350.193510.190210.25484RANDOM26.536
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]
1.261.26-2.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.608
r_dihedral_angle_4_deg22.039
r_dihedral_angle_3_deg19.431
r_dihedral_angle_1_deg7.279
r_scangle_it4.271
r_scbond_it2.742
r_angle_refined_deg1.826
r_mcangle_it1.61
r_mcbond_it0.924
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.608
r_dihedral_angle_4_deg22.039
r_dihedral_angle_3_deg19.431
r_dihedral_angle_1_deg7.279
r_scangle_it4.271
r_scbond_it2.742
r_angle_refined_deg1.826
r_mcangle_it1.61
r_mcbond_it0.924
r_nbtor_refined0.319
r_nbd_refined0.238
r_xyhbond_nbd_refined0.175
r_chiral_restr0.12
r_bond_refined_d0.02
r_gen_planes_refined0.006
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_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3548
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Cootmodel building
CCP4phasing