4LOG

The crystal structure of the orphan nuclear receptor PNR ligand binding domain fused with MBP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.6298PEG6000, pH 5.6, vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7955.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.435α = 90
b = 184.936β = 90
c = 85.97γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.0APS21-ID-D

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
12.73083.80.08520.5386833568522
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)
12.72.867.80.065524.5

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 id 3P0U (for PNR), pdb id 1OMP (for MBP)2.73035657295896.50.287120.285440.30744RANDOM51.63
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]
-0.59-0.951.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.484
r_dihedral_angle_4_deg17.523
r_dihedral_angle_3_deg17.114
r_sphericity_free12.158
r_sphericity_bonded8.254
r_scangle_it4.039
r_dihedral_angle_1_deg3.45
r_rigid_bond_restr3.397
r_scbond_it2.793
r_mcangle_it2.451
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.484
r_dihedral_angle_4_deg17.523
r_dihedral_angle_3_deg17.114
r_sphericity_free12.158
r_sphericity_bonded8.254
r_scangle_it4.039
r_dihedral_angle_1_deg3.45
r_rigid_bond_restr3.397
r_scbond_it2.793
r_mcangle_it2.451
r_mcbond_it1.325
r_angle_refined_deg1.145
r_angle_other_deg0.852
r_mcbond_other0.503
r_chiral_restr0.061
r_bond_refined_d0.01
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6172
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
DENZOdata reduction