9QRK | pdb_00009qrk

Structure of BromoCatch: Brd2BD2 L383A,D434C in complex with MR116.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	Morpheus: PEG 500 MME 40% (v/v), PEG 20,000 20 % (w/v), 0.12 M ethylene glycols, 0.1 M Tris-BICINE pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.13	α = 90
b = 71.64	β = 90
c = 32.05	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 16M	Beamsize: 20x20um	2024-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.6199	Diamond	I24

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	1.3	35.846	99.9	0.035	0.037	0.014	1	42.6	13.2		30315

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.33			0.096	0.104	0.039	0.997	20.7	13.2

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	1.3	35.846	30269	1503	99.917	0.148	0.147	0.1476	0.163	0.1628	12

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]
-0.179			-0.268		0.447

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.222
r_dihedral_angle_6_deg	17.028
r_dihedral_angle_3_deg	12.588
r_dihedral_angle_other_2_deg	11.333
r_dihedral_angle_1_deg	5.628
r_dihedral_angle_other_3_deg	5.522
r_lrange_it	4.738
r_lrange_other	4.584
r_scangle_it	3.262
r_scangle_other	3.26
r_angle_refined_deg	2.265
r_scbond_it	2.128
r_scbond_other	2.126
r_mcangle_other	1.748
r_mcangle_it	1.739
r_mcbond_it	1.19
r_mcbond_other	1.189
r_angle_other_deg	0.691
r_nbd_refined	0.236
r_nbtor_refined	0.199
r_symmetry_nbd_other	0.17
r_symmetry_nbd_refined	0.161
r_nbd_other	0.155
r_symmetry_xyhbond_nbd_refined	0.13
r_chiral_restr	0.105
r_xyhbond_nbd_refined	0.105
r_symmetry_nbtor_other	0.071
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	907
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
BUCCANEER	model building
xia2	data reduction