8HKR | pdb_00008hkr

Crystal Structure of Histone H3 Lysine 79 (H3K79) Methyltransferase Rv2067c from Mycobacterium tuberculosis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Determined using iodine SAD; experimental phasing

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Buffer: 0.1 M imidazole/MES acid, pH 6.5: Precipitant: 20% w/v polyethylene glycol 500* monomethyl ether + 10% w/v polyethylene glycol 20,000: Additive: 0.03 M sodium nitrate + 0.03 M sodium phosphate dibasic + 0.03 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.15	α = 90
b = 109.15	β = 90
c = 216.61	γ = 90

Symmetry
Space Group	P 41 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 PILATUS3 6M		2018-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.699996	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.4	48.81	100	0.089	0.09	0.999	24.37	25.383		51986			71.257

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.46	100		2.223	2.268	0.741	1.71	25.633

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	Determined using iodine SAD; experimental phasing	2.4	48.81	49385	2600	99.98	0.2025	0.2017	0.21	0.2183	0.22	RANDOM	66.041

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]
0.5			0.5		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.279
r_dihedral_angle_4_deg	16.414
r_dihedral_angle_3_deg	14.85
r_dihedral_angle_1_deg	7.05
r_mcangle_it	2.767
r_mcbond_it	1.77
r_mcbond_other	1.77
r_angle_refined_deg	1.337
r_angle_other_deg	1.19
r_chiral_restr	0.059

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.279
r_dihedral_angle_4_deg	16.414
r_dihedral_angle_3_deg	14.85
r_dihedral_angle_1_deg	7.05
r_mcangle_it	2.767
r_mcbond_it	1.77
r_mcbond_other	1.77
r_angle_refined_deg	1.337
r_angle_other_deg	1.19
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6068
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PHASER	phasing
CRANK2	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.