1XFF

Glutaminase domain of glucosamine 6-phosphate synthase complexed with glutamate


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
2.3647.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.38α = 90
b = 82.52β = 90
c = 86.05γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295IMAGE PLATEMARRESEARCHMIRROR1993-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.99EMBL/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
11.82499.90.06214.45.247043-318.3
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)
1.81.8297.10.28334.2

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 used1GPH1.820470184701899.80.16110.16110.16125.5
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]
0.98-0.64-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.769
r_scangle_it12.577
r_dihedral_angle_1_deg11.454
r_scbond_it9.906
r_mcangle_it6.945
r_mcbond_it4.496
r_angle_refined_deg1.728
r_nbtor_refined0.326
r_symmetry_vdw_refined0.31
r_nbd_refined0.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.769
r_scangle_it12.577
r_dihedral_angle_1_deg11.454
r_scbond_it9.906
r_mcangle_it6.945
r_mcbond_it4.496
r_angle_refined_deg1.728
r_nbtor_refined0.326
r_symmetry_vdw_refined0.31
r_nbd_refined0.239
r_symmetry_hbond_refined0.139
r_xyhbond_nbd_refined0.133
r_chiral_restr0.121
r_bond_refined_d0.015
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3746
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms26

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement