9GDK

Jumonji domain-containing protein 1C with crystallization epitope mutations L2440Y:G2444H

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	LFS well F04 20% PEG3350 10% ethylene glycol 0.1M bis-tris-propane pH 6.5 0.2M potassium thiocyanate

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.2	α = 90
b = 98.25	β = 92.04
c = 87.4	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 2M		2015-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.98	Diamond	I04-1

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	31.37	98.1	0.086	12	3.4		71577

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	1.83	99.4		0.936	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.78	31.369	71552	3511	97.995	0.211	0.2093	0.2422	33.142

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]
-1.142		-0.721	1.198		-0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	27.452
r_dihedral_angle_6_deg	15.601
r_dihedral_angle_3_deg	15.071
r_dihedral_angle_1_deg	7.4
r_dihedral_angle_2_deg	7.147
r_scangle_it	6.711
r_mcangle_it	4.922
r_scbond_it	4.372
r_mcbond_it	3.299
r_angle_refined_deg	1.859
r_symmetry_nbd_refined	0.491
r_nbd_refined	0.412
r_symmetry_xyhbond_nbd_refined	0.357
r_nbtor_refined	0.314
r_xyhbond_nbd_refined	0.28
r_chiral_restr	0.14
r_ncsr_local_group_1	0.115
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5267
Nucleic Acid Atoms
Solvent Atoms	607
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing