5NU6

Structure of non-fluorescent human amniotic fluid RBP4


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2934.3 M NaCl, 100 mM Hepes, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.5465.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.58α = 90
b = 102.58β = 90
c = 73.282γ = 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
11.6856.5395.30.0677.82.531219
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)
11.681.7793.70.4522.4

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 SYNTHESISTHROUGHOUT5NTY1.683029609160295.270.170890.169490.19711RANDOM42.121
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]
0.980.490.98-3.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.359
r_sphericity_bonded25.984
r_sphericity_free22.175
r_dihedral_angle_4_deg14.253
r_dihedral_angle_3_deg13.394
r_rigid_bond_restr12.412
r_scangle_other11.892
r_scbond_it11.819
r_scbond_other11.812
r_long_range_B_other11.474
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.359
r_sphericity_bonded25.984
r_sphericity_free22.175
r_dihedral_angle_4_deg14.253
r_dihedral_angle_3_deg13.394
r_rigid_bond_restr12.412
r_scangle_other11.892
r_scbond_it11.819
r_scbond_other11.812
r_long_range_B_other11.474
r_long_range_B_refined11.38
r_mcangle_it8.821
r_mcangle_other8.744
r_dihedral_angle_1_deg8.207
r_mcbond_other8.179
r_mcbond_it8.111
r_angle_other_deg1.118
r_angle_refined_deg0.684
r_chiral_restr0.037
r_bond_other_d0.006
r_bond_refined_d0.003
r_gen_planes_refined0.002
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 Atoms89
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling