Experiment: 4UC4

Crystal structure of hybrid tudor domain of human lysine demethylase KDM4B

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GF7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	288	0.06M Divalents (MgCl2/CaCl2), 0.1M Buffer pH8.5 (TRIS/Bicine) and 30% w/v EDO/P8K

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.436	α = 90
b = 77.436	β = 90
c = 50.758	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2014-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.56	30	100	0.11	6.5	6.5		10956			44.83

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	2.56	2.6	100		0.813		6.3	542

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2GF7	2.5612	27.977	1.99	10939	1177	99.95	0.2034	0.1973	0.2055	0.2544	0.2569	Random selection	48.0444

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.294
f_angle_d	1.122
f_chiral_restr	0.044
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1716
Nucleic Acid Atoms
Solvent Atoms	66
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data reduction
PHENIX	phasing
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling