5NU8

Structure of human urine RBP4 saturated with palmitate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NU2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	4.3 M NaCl, 100 mM Hepes, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.57	65.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.79	α = 90
b = 102.79	β = 90
c = 73.634	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2016-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.0	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.59	56.74	90.9	0.053	9.2	2.5		35401

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.59	1.68	92.3		0.466	2	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5NU2	1.59	30	33661	1733	90.86	0.17203	0.16999	0.21167	RANDOM	45.439

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]
0.18	0.09		0.18		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.515
r_sphericity_bonded	22.474
r_sphericity_free	18.729
r_dihedral_angle_4_deg	16.048
r_dihedral_angle_3_deg	14.933
r_rigid_bond_restr	13.296
r_long_range_B_other	12.423
r_long_range_B_refined	12.295
r_scangle_other	11.096
r_scbond_it	10.665
r_scbond_other	10.658
r_mcangle_it	9.195
r_mcangle_other	9.195
r_mcbond_it	8.709
r_mcbond_other	8.703
r_dihedral_angle_1_deg	8.089
r_angle_other_deg	1.111
r_angle_refined_deg	0.643
r_chiral_restr	0.038
r_bond_other_d	0.006
r_bond_refined_d	0.003
r_gen_planes_refined	0.002
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 Atoms	Number
Protein Atoms	1408
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing