1LEV

PORCINE KIDNEY FRUCTOSE-1,6-BISPHOSPHATASE COMPLEXED WITH AN AMP-SITE INHIBITOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FBPPDB ENTRY 1FBP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72980.2M Na Acetate, 13.75% PEG 4000, 0.1M Hepes pH7.0, 1mM F6P, 2mM MnCl2, 1mM inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2344.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.87α = 90
b = 73.446β = 106.3
c = 78.025γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IICmirrors1999-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.1540.2693.80.1061332736-3
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)
12.152.2364.50.4832.442.32255

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1FBP2.1540.263273432734163993.620.195820.195820.192690.25514RANDOM31.619
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]
0.35-1.12-0.13-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg23.573
r_scangle_it7.059
r_dihedral_angle_1_deg5.056
r_scbond_it4.894
r_mcangle_it4.295
r_angle_refined_deg3.04
r_mcbond_it2.49
r_angle_other_deg1.661
r_symmetry_vdw_other0.422
r_symmetry_vdw_refined0.366
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg23.573
r_scangle_it7.059
r_dihedral_angle_1_deg5.056
r_scbond_it4.894
r_mcangle_it4.295
r_angle_refined_deg3.04
r_mcbond_it2.49
r_angle_other_deg1.661
r_symmetry_vdw_other0.422
r_symmetry_vdw_refined0.366
r_nbd_other0.25
r_nbd_refined0.244
r_symmetry_hbond_refined0.242
r_chiral_restr0.168
r_xyhbond_nbd_refined0.148
r_nbtor_other0.106
r_xyhbond_nbd_other0.073
r_bond_refined_d0.02
r_gen_planes_refined0.013
r_gen_planes_other0.007
r_bond_other_d0.003
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4767
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms74

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement