2IQY

Rat Phosphatidylethanolamine-Binding Protein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2M Cacl2, HEPES pH 7.5 and 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.9336.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.694α = 90
b = 70.588β = 109.96
c = 38.672γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-3mirrors2006-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-BM

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
11.426.2389.30.04213.63.92814028140
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)
1.41.4548.20.1037.452.51510

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 2IQX1.426.232528125281283889.310.153210.153210.148790.19299RANDOM12.223
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]
-0.29-0.070.26-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.718
r_dihedral_angle_3_deg13.602
r_dihedral_angle_4_deg12.947
r_dihedral_angle_1_deg6.284
r_scangle_it2.799
r_scbond_it1.969
r_angle_refined_deg1.458
r_mcangle_it1.363
r_mcbond_it0.821
r_nbd_refined0.264
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.718
r_dihedral_angle_3_deg13.602
r_dihedral_angle_4_deg12.947
r_dihedral_angle_1_deg6.284
r_scangle_it2.799
r_scbond_it1.969
r_angle_refined_deg1.458
r_mcangle_it1.363
r_mcbond_it0.821
r_nbd_refined0.264
r_xyhbond_nbd_refined0.237
r_symmetry_hbond_refined0.236
r_symmetry_vdw_refined0.194
r_chiral_restr0.105
r_metal_ion_refined0.049
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
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 Atoms1686
Nucleic Acid Atoms
Solvent Atoms402
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing