9I2L | pdb_00009i2l

BtuJ2 - DUF4465 domain containing protein

X-RAY DIFFRACTION

---

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	3.5	293	29% w/v PEG, 0.2M sodium citrate pH 3.5

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.746	α = 90
b = 97.98	β = 90
c = 70.472	γ = 90

Symmetry
Space Group	P 21 21 2

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 9M		2024-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	1.6	81.09	82	0.2	0.2	0.1	0.968	1.7	4.4		66258			13.12

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	1.6	1.7			0.381

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	2.73	70.472	15635	754	97.89	0.188	0.1849	0.1851	0.2609	0.2608	38.391

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]
-0.42			0.951		-0.531

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.829
r_dihedral_angle_3_deg	12.952
r_dihedral_angle_2_deg	11.282
r_lrange_it	9.555
r_lrange_other	9.555
r_dihedral_angle_1_deg	8.633
r_scangle_it	7.806
r_scangle_other	7.805
r_mcangle_other	6.918
r_mcangle_it	6.917
r_scbond_it	5.311
r_scbond_other	5.31
r_mcbond_it	4.751
r_mcbond_other	4.751
r_angle_refined_deg	2.506
r_angle_other_deg	1.024
r_metal_ion_refined	0.315
r_nbd_refined	0.203
r_nbtor_refined	0.183
r_symmetry_nbd_other	0.178
r_nbd_other	0.173
r_symmetry_nbd_refined	0.168
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.116
r_symmetry_xyhbond_nbd_refined	0.108
r_ncsr_local_group_1	0.106
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4069
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	188

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing