5NUB

Structure of human amniotic fluid RBP4 saturated with laurate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NU6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2934.3 M NaCl, 100 mM Hepes, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.5365.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.61α = 90
b = 102.61β = 90
c = 73.134γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.0ESRFID29

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
11.656.4799.30.05412.84.637622
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)
11.61.6998.70.4812.64.2

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5NU61.63035652195399.240.17520.173550.20495RANDOM40.874
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]
1.060.531.06-3.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.064
r_sphericity_bonded17.833
r_dihedral_angle_4_deg16.347
r_sphericity_free15.48
r_dihedral_angle_3_deg14.206
r_rigid_bond_restr13.59
r_dihedral_angle_1_deg8.589
r_long_range_B_other7.921
r_long_range_B_refined7.832
r_scbond_it7.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.064
r_sphericity_bonded17.833
r_dihedral_angle_4_deg16.347
r_sphericity_free15.48
r_dihedral_angle_3_deg14.206
r_rigid_bond_restr13.59
r_dihedral_angle_1_deg8.589
r_long_range_B_other7.921
r_long_range_B_refined7.832
r_scbond_it7.66
r_scbond_other7.655
r_scangle_other7.588
r_mcangle_it6.782
r_mcangle_other6.774
r_mcbond_it6.065
r_mcbond_other6.06
r_angle_other_deg0.982
r_angle_refined_deg0.678
r_chiral_restr0.042
r_bond_other_d0.005
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_gen_planes_other
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1408
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing