5FPD

Structure of heat shock-related 70kDA protein 2 with small-molecule ligand pyrazine-2-carboxamide (AT513) in an alternate binding site.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
181.0M NACL, 0.1M TRIS/HCL PH=8, 20.0% W/V PEG 8000. PROTEIN CONC. = 9MG/ML.
Crystal Properties
Matthew coefficientSolvent content
2.3146.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.8α = 90
b = 95.062β = 90.03
c = 81.779γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU SATURN CCDMIRRORS2008-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+

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
11.9738.397.90.0512.7253188-3.722.79
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)
11.972.0388.40.163.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1S3X1.9738.3451667263897.90.17290.17020.2229RANDOM23.45
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]
0.5050.06431.3281-1.8331
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion15.66
t_omega_torsion5.51
t_angle_deg1.01
t_bond_d0.012
t_improper_torsion
t_pseud_angle
t_gen_planes
t_it
t_nbd
t_incorr_chiral_ct
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion15.66
t_omega_torsion5.51
t_angle_deg1.01
t_bond_d0.012
t_improper_torsion
t_pseud_angle
t_gen_planes
t_it
t_nbd
t_incorr_chiral_ct
t_dihedral_angle_d
t_trig_c_planes
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5775
Nucleic Acid Atoms
Solvent Atoms878
Heterogen Atoms18

Software

Software
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing