6KZR

Crystal structure of mouse DCAR2 CRD domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LFJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	PEG

Crystal Properties
Matthews coefficient	Solvent content
4	69.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.979	α = 90
b = 72.435	β = 90
c = 101.106	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210		2018-12-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.000	SPring-8	BL26B1

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	1.84	58.9	99.7	0.12	15.1	7.2		22002

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.44			0.687	0.867	2.99

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	6LFJ	2.304	43.971	22002	1141	99.724	0.19	0.1888	0.2207	34.626

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]
0.237			-0.178		-0.059

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.397
r_dihedral_angle_3_deg	15.537
r_lrange_it	12.208
r_lrange_other	12.201
r_dihedral_angle_4_deg	11.376
r_scangle_it	7.691
r_scangle_other	7.689
r_dihedral_angle_1_deg	6.94
r_mcangle_it	5.777
r_mcangle_other	5.775
r_scbond_it	5.015
r_scbond_other	5.013
r_mcbond_it	3.754
r_mcbond_other	3.742
r_angle_other_deg	2.37
r_angle_refined_deg	1.407
r_symmetry_nbd_refined	0.29
r_nbd_other	0.229
r_symmetry_nbd_other	0.216
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.171
r_metal_ion_refined	0.09
r_symmetry_xyhbond_nbd_refined	0.078
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.064
r_bond_other_d	0.036
r_bond_refined_d	0.007
r_gen_planes_other	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2172
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing