7AA0

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

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.55	α = 90
b = 49.92	β = 96.03
c = 67.38	γ = 90

Symmetry
Space Group	P 1 21 1

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 PILATUS3 6M		2018-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.82	49.92	97.6	0.065	0.089	0.061	0.996	10.4	3.5		23023

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	1.82	1.86			0.735	1.003	0.678	0.486		3.7

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	5OGB	1.82	40.064	23016	1125	97.53	0.199	0.1967	0.2452	29.068

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]
-0.042		0.705	-1.062		0.934

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.454
r_dihedral_angle_3_deg	14.034
r_dihedral_angle_4_deg	14.029
r_dihedral_angle_1_deg	7.953
r_lrange_it	6.655
r_lrange_other	6.633
r_scangle_it	5.265
r_scangle_other	5.264
r_mcangle_other	3.303
r_mcangle_it	3.3
r_scbond_other	3.287
r_scbond_it	3.286
r_mcbond_it	2.296
r_mcbond_other	2.292
r_angle_refined_deg	1.55
r_angle_other_deg	1.281
r_symmetry_xyhbond_nbd_refined	0.308
r_symmetry_nbd_refined	0.199
r_nbd_other	0.191
r_xyhbond_nbd_refined	0.19
r_nbd_refined	0.186
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.163
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_other	0.015
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2178
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	52

Software

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