9L1J | pdb_00009l1j

sdAbB YERLA mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293.15	0.1M HEPES Sodium, 2% PEG400, 1.5M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.929	α = 90
b = 77.929	β = 90
c = 45.283	γ = 120

Symmetry
Space Group	P 3 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	100	PIXEL	DECTRIS PILATUS3 S 6M		2024-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.62	45.3	100	0.072	0.025	0.998	16.3	9.9		20480

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.62	1.65			0.898	0.295	0.787	2.6

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.62	45.283	20477	1002	99.971	0.161	0.1597	0.1705	0.1994	0.2094	30.05

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]
-0.119	-0.06		-0.119		0.387

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	17.416
r_lrange_other	16.531
r_dihedral_angle_6_deg	14.686
r_dihedral_angle_3_deg	12.065
r_scangle_it	11.821
r_scangle_other	11.813
r_mcangle_it	11.394
r_mcangle_other	11.394
r_dihedral_angle_2_deg	8.012
r_scbond_it	7.997
r_scbond_other	7.989
r_dihedral_angle_1_deg	7.685
r_mcbond_it	7.54
r_mcbond_other	7.52
r_rigid_bond_restr	2.92
r_angle_refined_deg	1.44
r_angle_other_deg	0.502
r_xyhbond_nbd_refined	0.253
r_nbd_other	0.226
r_nbd_refined	0.218
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.184
r_symmetry_nbd_refined	0.127
r_symmetry_xyhbond_nbd_refined	0.094
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.068
r_gen_planes_refined	0.007
r_bond_refined_d	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	893
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	33

Software

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