2J5V

GLUTAMATE 5-KINASE FROM ESCHERICHIA COLI COMPLEXED WITH GLUTAMYL-5-PHOSPHATE AND PYROGLUTAMIC ACID


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AKOPDB ENTRY 2AKO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.51.6 M MGSO4, 0.1 M KCL, 0.1 M MES PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.9257.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.455α = 90
b = 101.455β = 90
c = 178.728γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHA RD COATED FLAT MIRROR AND A RD COATED TOROIDAL MIRROR2003-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM16ESRFBM16

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
12.548.899.50.076.811.1615661.7
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)
12.52.6499.50.421.76.2

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 2AKO2.588.3931155166799.50.1950.1920.244RANDOM37.04
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]
0.320.32-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.844
r_dihedral_angle_4_deg20.091
r_dihedral_angle_3_deg17.168
r_dihedral_angle_1_deg5.868
r_scangle_it2.639
r_scbond_it1.592
r_angle_refined_deg1.353
r_mcangle_it0.898
r_mcbond_it0.515
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.844
r_dihedral_angle_4_deg20.091
r_dihedral_angle_3_deg17.168
r_dihedral_angle_1_deg5.868
r_scangle_it2.639
r_scbond_it1.592
r_angle_refined_deg1.353
r_mcangle_it0.898
r_mcbond_it0.515
r_nbtor_refined0.297
r_nbd_refined0.207
r_xyhbond_nbd_refined0.172
r_symmetry_vdw_refined0.136
r_symmetry_hbond_refined0.125
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.004
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 Atoms4866
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing