8YHS | pdb_00008yhs

The Crystal Structure of BRDT from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RFJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	18 % PEG 3350, 0.1 M CAPSO 9.0, 17 % PEG 400, 4.8 % 2-Propanol

Crystal Properties
Matthews coefficient	Solvent content
2.14	37.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.567	α = 90
b = 44.38	β = 90
c = 72.125	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	PIXEL	DECTRIS PILATUS3 6M		2022-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00000	SPring-8	BL45XU

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	1.5	44.38	100	0.093	12.8	7.8		18434

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53			0.879

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	FREE R-VALUE	1.5	37.798	18383	916	99.956	0.186	0.1845	0.2	0.2217	0.23	20.51

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]
-1.917			-1.675		3.592

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.14
r_dihedral_angle_4_deg	13.871
r_dihedral_angle_3_deg	13.578
r_lrange_it	5.755
r_lrange_other	5.722
r_dihedral_angle_1_deg	5.617
r_scangle_it	4.321
r_scangle_other	4.319
r_scbond_it	2.722
r_scbond_other	2.719
r_mcangle_it	2.583
r_mcangle_other	2.581
r_mcbond_it	1.707
r_mcbond_other	1.706
r_angle_refined_deg	1.527
r_angle_other_deg	1.359
r_nbd_refined	0.209
r_nbd_other	0.203
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.181
r_symmetry_nbd_refined	0.165
r_symmetry_nbd_other	0.157
r_symmetry_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_other	0.142
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	905
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	36

Software

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