4UF0 | pdb_00004uf0

Crystal structure of JmjC domain of human histone demethylase UTY in complex with epitherapuetic compound 2-(((2-((2-(dimethylamino)ethyl) (ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinic acid.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZLI	PDB ENTRY 3ZLI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		25% PEG3350, 0.1M BIS-TRIS PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.494	α = 90
b = 110.458	β = 90
c = 119.23	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	287	CCD	ADSC CCD	ADSC QUANTUM 315	2014-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	1.78	81.03	99.9	0.06	19.51	6.7		114771		2

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	1.78	1.84	99.9		0.06	2.86	6.8

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	PDB ENTRY 3ZLI	1.78	81.03	109117	5650	99.97	0.15184	0.14857	0.16	0.21517	0.23	RANDOM	36.64

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]
-1.63			0.49		1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.489
r_sphericity_free	28.313
r_sphericity_bonded	18.008
r_dihedral_angle_4_deg	15.561
r_dihedral_angle_3_deg	13.89
r_scbond_it	7.072
r_dihedral_angle_1_deg	6.389
r_mcangle_it	6.02
r_rigid_bond_restr	5.478
r_mcbond_it	5.359
r_mcbond_other	5.358
r_angle_refined_deg	1.714
r_angle_other_deg	0.909
r_chiral_restr	0.101
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7058
Nucleic Acid Atoms
Solvent Atoms	488
Heterogen Atoms	128

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
CCP4I	phasing