7D0Q | pdb_00007d0q

Crystal structure of human HBO1-BRPF2 in complex with butyryl-coenzyme A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GK9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.1 M Tris, pH 8.5, 20% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.871	α = 90
b = 39.599	β = 122.89
c = 87.9	γ = 90

Symmetry
Space Group	C 1 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 6M		2018-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97892	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	50.01	99.3	0.09	1	28.6	6.6		18377

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28			0.56	0.95	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5GK9	2.21	50.01	17452	925	98.2	0.1889	0.186	0.1862	0.2435	0.2439	RANDOM	69.279

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]
-2.87		-0.9	2.39		0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.867
r_sphericity_bonded	37.881
r_sphericity_free	35.277
r_dihedral_angle_4_deg	21.888
r_dihedral_angle_3_deg	17.598
r_rigid_bond_restr	7.768
r_dihedral_angle_1_deg	6.035
r_angle_refined_deg	1.212
r_chiral_restr	0.059
r_bond_refined_d	0.007
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2480
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing