2JG5

CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOFRUCTOKINASE FROM STAPHYLOCOCCUS AUREUS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ABQPDB ENTRY 2ABQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.60.2 M AMMONIUM ACETATE, 0.1M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 30% W/V PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.0440

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.01α = 90
b = 160.26β = 90
c = 40.74γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2006-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.283098.10.1111.654.8254861
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)
12.282.4298.10.1111.654.8

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 2ABQ2.319.7524100129099.50.2150.2120.276RANDOM32.32
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]
-0.09-0.050.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.892
r_dihedral_angle_4_deg19.671
r_dihedral_angle_3_deg14.99
r_dihedral_angle_1_deg5.862
r_scangle_it1.58
r_angle_refined_deg1.195
r_scbond_it0.994
r_mcangle_it0.644
r_mcbond_it0.381
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.892
r_dihedral_angle_4_deg19.671
r_dihedral_angle_3_deg14.99
r_dihedral_angle_1_deg5.862
r_scangle_it1.58
r_angle_refined_deg1.195
r_scbond_it0.994
r_mcangle_it0.644
r_mcbond_it0.381
r_nbtor_refined0.3
r_symmetry_vdw_refined0.227
r_nbd_refined0.205
r_symmetry_hbond_refined0.163
r_xyhbond_nbd_refined0.134
r_chiral_restr0.076
r_bond_refined_d0.011
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 Atoms4572
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing