7A9Y

Structural comparison of cellular retinoic acid binding protein 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	1CBR

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.89	α = 90
b = 109.98	β = 90
c = 170.34	γ = 90

Symmetry
Space Group	I 2 2 2

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		2018-10-03	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	1.64	36.05	99.9	0.029	0.029	0.029	0.999	9.8	1.9		43110

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	1.64	1.67			0.791	0.559	0.559	0.48		1.9

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	1CBR	1.64	36.05	43108	2049	99.861	0.193	0.1914	0.2184	35.424

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]
0.028			0.248		-0.277

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.657
r_dihedral_angle_4_deg	17.956
r_dihedral_angle_3_deg	14.001
r_lrange_it	9.073
r_lrange_other	9.067
r_scangle_it	7.779
r_scangle_other	7.777
r_dihedral_angle_1_deg	6.95
r_scbond_it	5.098
r_scbond_other	5.096
r_mcangle_it	4.661
r_mcangle_other	4.66
r_mcbond_it	3.44
r_mcbond_other	3.439
r_angle_refined_deg	1.699
r_angle_other_deg	1.433
r_symmetry_xyhbond_nbd_refined	0.629
r_symmetry_nbd_refined	0.285
r_xyhbond_nbd_refined	0.211
r_nbd_other	0.208
r_nbd_refined	0.198
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.166
r_ncsr_local_group_1	0.115
r_symmetry_nbtor_other	0.095
r_chiral_restr	0.087
r_symmetry_xyhbond_nbd_other	0.082
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	2171
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	37

Software

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