2AJR

Crystal structure of Possible 1-phosphofructokinase (EC 2.7.1.56) (tm0828) from Thermotoga Maritima at 2.46 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.529316% PEG-8000, 0.08M sodium cacodylate, 0.16M magnesium acetate tetrahydrate, 20% glyerol anhyrous , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.9457.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.796α = 90
b = 115.796β = 90
c = 124.828γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315FLAT MIRROR2002-06-17MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.885567,0.976224SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.429.299.50.1090.1095.96.331322
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.462.52950.6330.6331.23.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.4628.4929692159599.40.1930.24RANDOM31.77
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]
1.311.31-2.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.829
r_dihedral_angle_3_deg17.005
r_dihedral_angle_4_deg15.688
r_scangle_it6.864
r_dihedral_angle_1_deg6.194
r_scbond_it5.131
r_mcangle_it2.525
r_mcbond_it1.719
r_angle_refined_deg1.274
r_angle_other_deg0.825
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.829
r_dihedral_angle_3_deg17.005
r_dihedral_angle_4_deg15.688
r_scangle_it6.864
r_dihedral_angle_1_deg6.194
r_scbond_it5.131
r_mcangle_it2.525
r_mcbond_it1.719
r_angle_refined_deg1.274
r_angle_other_deg0.825
r_mcbond_other0.391
r_nbd_refined0.204
r_symmetry_vdw_other0.204
r_nbd_other0.183
r_nbtor_refined0.181
r_symmetry_hbond_refined0.159
r_symmetry_vdw_refined0.158
r_xyhbond_nbd_refined0.148
r_nbtor_other0.086
r_chiral_restr0.073
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5013
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
SnBphasing
MLPHAREphasing
SOLVEphasing