1U29

Triglycine variant of the ARNO Pleckstrin Homology Domain in complex with Ins(1,4,5)P3


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293PEG 4000, Hepes, 10% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3146.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.998α = 90
b = 56.378β = 90
c = 57.091γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2001-03-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.82099.61345613437-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8599.4

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 REPLACEMENTTHROUGHOUT1FGY1.820127271272766099.830.23040.230380.228770.26225RANDOM25.493
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]
0.93-1.680.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.02
r_scangle_it2.919
r_scbond_it1.902
r_mcangle_it1.4
r_angle_refined_deg1.203
r_angle_other_deg0.748
r_mcbond_it0.747
r_symmetry_vdw_other0.305
r_nbd_other0.241
r_nbd_refined0.177
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.02
r_scangle_it2.919
r_scbond_it1.902
r_mcangle_it1.4
r_angle_refined_deg1.203
r_angle_other_deg0.748
r_mcbond_it0.747
r_symmetry_vdw_other0.305
r_nbd_other0.241
r_nbd_refined0.177
r_symmetry_hbond_refined0.137
r_xyhbond_nbd_refined0.134
r_symmetry_vdw_refined0.103
r_nbtor_other0.08
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms977
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing