2PHN

Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G9IPDB entry 2G9I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62890.2 M Ammonium acetate, 0.1 M Sodium citrate, 25% PEG 5000 MME, 10 mM GDP, MnCl2, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0540.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.367α = 90
b = 98.367β = 90
c = 94.347γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2006-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97940APS19-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
11.354098.70.05522.38.29972799727
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)
11.351.3797.90.494.697.54897

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2G9I1.35409972794754497398.340.1640.161790.16030.18997RANDOM15.446
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]
0.410.41-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.187
r_dihedral_angle_4_deg19.515
r_dihedral_angle_3_deg12.472
r_dihedral_angle_1_deg6.235
r_sphericity_free5.961
r_scangle_it3.703
r_sphericity_bonded3.238
r_scbond_it2.629
r_rigid_bond_restr2.306
r_mcangle_it2.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.187
r_dihedral_angle_4_deg19.515
r_dihedral_angle_3_deg12.472
r_dihedral_angle_1_deg6.235
r_sphericity_free5.961
r_scangle_it3.703
r_sphericity_bonded3.238
r_scbond_it2.629
r_rigid_bond_restr2.306
r_mcangle_it2.009
r_angle_refined_deg1.564
r_mcbond_it1.493
r_angle_other_deg0.955
r_mcbond_other0.581
r_symmetry_vdw_other0.333
r_symmetry_vdw_refined0.248
r_nbd_refined0.226
r_symmetry_hbond_refined0.218
r_nbd_other0.206
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.168
r_chiral_restr0.092
r_nbtor_other0.086
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3809
Nucleic Acid Atoms
Solvent Atoms576
Heterogen Atoms98

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing