3DRW

Crystal Structure of a Phosphofructokinase from Pyrococcus horikoshii OT3 with AMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U2X1U2X molecule A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29320% PEG 3350, 0.2 M Lithium Citrate plus 5 mM ADP Cryoprotected in N-paratone oil., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2445.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.464α = 90
b = 104.19β = 105.09
c = 70.844γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97929APS19-ID

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
11.95098.70.0816.74.5758387481523.5
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)
11.91.9790.70.3533.23.96856

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1U2X molecule A1.941.457477571005377098.270.174260.171610.2244RANDOM29.37
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]
-0.050.030.1-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.107
r_dihedral_angle_4_deg18.377
r_dihedral_angle_3_deg15.637
r_dihedral_angle_1_deg7.542
r_scangle_it5.917
r_scbond_it3.545
r_mcangle_it1.991
r_angle_refined_deg1.8
r_mcbond_it1.082
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.107
r_dihedral_angle_4_deg18.377
r_dihedral_angle_3_deg15.637
r_dihedral_angle_1_deg7.542
r_scangle_it5.917
r_scbond_it3.545
r_mcangle_it1.991
r_angle_refined_deg1.8
r_mcbond_it1.082
r_nbtor_refined0.316
r_nbd_refined0.22
r_symmetry_vdw_refined0.215
r_chiral_restr0.165
r_symmetry_hbond_refined0.153
r_xyhbond_nbd_refined0.15
r_bond_refined_d0.02
r_gen_planes_refined0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7379
Nucleic Acid Atoms
Solvent Atoms576
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing