Experiment: 5NFO

Human JMJD7 in complex with Mn and 2OG in the P21212 form

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298	26 mg/mL His6-JMJD7-R260C, 2 mM MnCl2, 4 mM 2OG, 1.5 M Sodium Nitrate, 0.1 M Sodium Acetate pH 4.6 and additives (0.25% beta-NADP, 0.25% ATP, 0.25% N-Acetyl-D-galactosamine, 0.25% Gentamicin sulfate, 0.02 M HEPES-Na pH 6.8)

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.315	α = 90
b = 61.02	β = 90
c = 86.055	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 PILATUS3 6M	MIRRORS	2016-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9795	Diamond	I03

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	2.17	49.776	100	0.131	13.2857	9		38951			35.1

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	2.17	2.23	100		1.176	1.75	9.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5NFN	2.173	49.776	1.34	38901	1919	99.97	0.1728	0.171	0.1931	0.189	0.1906	46

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]
-0.87			11.57		-10.7

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.966
f_angle_d	1.21
f_chiral_restr	0.048
f_bond_d	0.01
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5025
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	66

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing