7AJL | pdb_00007ajl

Cyrstal structure of CYRI-B/Fam49B

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1M carboxylic acid, 8% MPD_P1K_P33 0.1M MOPS/HEPES-Na pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.731	α = 90
b = 166.686	β = 112.343
c = 45.131	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	100	PIXEL	DECTRIS EIGER X 16M		2019-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.37	83.343	99.94	0.97	25	23		24725

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.37	2.45			0.97

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.37	83.343	24725	1242	100	0.205	0.2025	0.2239	0.2454	0.2603	78.043

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]
13.654		3.214	-10.043		-4.674

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.828
r_dihedral_angle_3_deg	19.037
r_dihedral_angle_4_deg	18.699
r_lrange_other	12.16
r_lrange_it	12.157
r_scangle_it	8.656
r_scangle_other	8.655
r_mcangle_it	7.892
r_mcangle_other	7.891
r_dihedral_angle_1_deg	7.804
r_scbond_it	5.572
r_scbond_other	5.551
r_mcbond_it	5.302
r_mcbond_other	5.302
r_angle_other_deg	1.065
r_angle_refined_deg	1.001
r_nbd_other	0.282
r_symmetry_nbd_other	0.242
r_symmetry_nbd_refined	0.235
r_symmetry_xyhbond_nbd_refined	0.216
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.2
r_ncsr_local_group_1	0.165
r_nbtor_refined	0.163
r_symmetry_xyhbond_nbd_other	0.1
r_xyhbond_nbd_other	0.099
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.025
r_bond_other_d	0.002
r_gen_planes_refined	0.002
r_bond_refined_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4552
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
DIALS	data scaling
PHASER	phasing