1XFG

Glutaminase domain of glucosamine 6-phosphate synthase complexed with l-glu hydroxamate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GPH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52950.1 M cacodylate, 1 M sodium acetate, 20% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3447.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.25α = 90
b = 82.4β = 90
c = 85.83γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295IMAGE PLATEMARRESEARCHMIRROR1993-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.9300EMBL/DESY, HAMBURGX11

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
11.851599.60.05315.24.44293042930-318.4
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)
1.851.992.30.2623.24

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTnone used1GPH1.8515429304293099.60.1590.1590.15926.6
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]
1.11-0.72-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.984
r_scangle_it12.947
r_dihedral_angle_1_deg11.45
r_scbond_it10.125
r_mcangle_it7.256
r_mcbond_it5.026
r_angle_refined_deg1.83
r_nbtor_refined0.331
r_nbd_refined0.246
r_symmetry_vdw_refined0.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.984
r_scangle_it12.947
r_dihedral_angle_1_deg11.45
r_scbond_it10.125
r_mcangle_it7.256
r_mcbond_it5.026
r_angle_refined_deg1.83
r_nbtor_refined0.331
r_nbd_refined0.246
r_symmetry_vdw_refined0.209
r_xyhbond_nbd_refined0.144
r_symmetry_hbond_refined0.144
r_chiral_restr0.127
r_bond_refined_d0.016
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3695
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms32

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement