4CN3

Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human Gde1SpA Response Element


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DSZPDB ENTRY 1DSZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.1120% PEG 3350, 0.2M NH4CL, pH 6.11
Crystal Properties
Matthews coefficientSolvent content
2.0446.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.91α = 90
b = 69.28β = 90
c = 138.86γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2010-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.369.695.10.149.7623573-341.34
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)
12.32.4286.80.473.55.6

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 1DSZ2.3524.5720297104092.430.18310.17940.2493RANDOM28.15
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]
7.207-0.277-6.93
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion18.97
t_omega_torsion2.92
t_angle_deg1.23
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion18.97
t_omega_torsion2.92
t_angle_deg1.23
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
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 Atoms2574
Nucleic Acid Atoms1382
Solvent Atoms323
Heterogen Atoms8

Software

Software
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing