1U2B

Triglycine variant of the Grp1 Pleckstrin Homology Domain unliganded


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.2293PEG 4000, sodium acetate, 10% glycerol, lithium sulfate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7355

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.794α = 90
b = 107.514β = 90
c = 37.359γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2000-09-19MSINGLE 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
11.85098.61593715719-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8596.8

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 REPLACEMENTTHROUGHOUT1FGY1.820150861489978498.760.218970.218970.217860.24004RANDOM23.028
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]
-0.60.82-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.985
r_scangle_it2.66
r_scbond_it1.618
r_mcangle_it1.424
r_angle_refined_deg1.136
r_mcbond_it0.766
r_angle_other_deg0.724
r_symmetry_vdw_other0.267
r_nbd_other0.243
r_nbd_refined0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.985
r_scangle_it2.66
r_scbond_it1.618
r_mcangle_it1.424
r_angle_refined_deg1.136
r_mcbond_it0.766
r_angle_other_deg0.724
r_symmetry_vdw_other0.267
r_nbd_other0.243
r_nbd_refined0.19
r_xyhbond_nbd_refined0.17
r_symmetry_vdw_refined0.158
r_symmetry_hbond_refined0.096
r_nbtor_other0.082
r_chiral_restr0.07
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 Atoms1057
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing