7AA1

Structural comparison of cellular retinoic acid binding proteins I and II in the presence and absence of natural and synthetic ligands

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	PEG based vapor diffusion

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.56	α = 90
b = 78.56	β = 90
c = 78.56	γ = 90

Symmetry
Space Group	P 21 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	PIXEL	DECTRIS PILATUS 6M		2019-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9763	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.71	45.398	100	0.077	0.082	0.026	0.999	18.8	18.3		17775

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.71	1.74			2.227	2.356	0.76	0.548		18.3

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5OBG	1.71	45.398	17753	889	99.955	0.181	0.1802	0.2011	37.241

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.326
r_dihedral_angle_3_deg	13.769
r_dihedral_angle_4_deg	12.3
r_lrange_it	7.715
r_lrange_other	7.712
r_dihedral_angle_1_deg	7.502
r_scangle_it	6.876
r_scangle_other	6.872
r_scbond_it	4.475
r_scbond_other	4.473
r_mcangle_other	4.063
r_mcangle_it	4.048
r_mcbond_it	3.231
r_mcbond_other	3.079
r_angle_refined_deg	1.754
r_angle_other_deg	1.421
r_symmetry_nbd_refined	0.338
r_nbd_refined	0.199
r_symmetry_nbd_other	0.182
r_symmetry_xyhbond_nbd_refined	0.181
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.161
r_nbd_other	0.133
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1091
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data reduction
XDS	data processing
PHASER	phasing
Coot	model building