7A9Z

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
3.93	68.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.545	α = 90
b = 127.545	β = 90
c = 52.161	γ = 120

Symmetry
Space Group	P 31 2 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 PILATUS 6M		2020-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9763	Diamond	I04

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	2.41	110.46	99.9	0.107	0.392	0.123	0.994	7.1	19.2		19102

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	2.41	2.5			6.347	6.751	2.287	0.398		16.8

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	2.41	110.457	19078	848	99.806	0.207	0.2047	0.25	53.96

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]
1.143	0.572		1.143		-3.709

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.452
r_dihedral_angle_3_deg	17.666
r_dihedral_angle_4_deg	16.601
r_lrange_other	11.723
r_lrange_it	11.718
r_scangle_other	8.258
r_scangle_it	8.255
r_dihedral_angle_1_deg	8.06
r_mcangle_other	7.338
r_mcangle_it	7.332
r_scbond_other	5.159
r_scbond_it	5.158
r_mcbond_it	4.764
r_mcbond_other	4.747
r_angle_refined_deg	1.559
r_angle_other_deg	1.28
r_symmetry_nbd_refined	0.378
r_nbd_other	0.209
r_nbd_refined	0.195
r_symmetry_nbd_other	0.183
r_xyhbond_nbd_refined	0.171
r_nbtor_refined	0.164
r_ncsr_local_group_1	0.154
r_symmetry_xyhbond_nbd_refined	0.145
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.064
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2141
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	25

Software

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