9GP4

Jumonji domain-containing protein 2A with crystallization epitope mutations Q953E:A958D

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GD4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2M ammonium sulfate, 0.1M bis-tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
3.95	68.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.1	α = 90
b = 136.1	β = 90
c = 136.1	γ = 90

Symmetry
Space Group	I 41 3 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 PILATUS 6M		2015-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.916	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.58	96.23	100	1	25.9	38.2		29690

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.62			0.803

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.59	55.624	29114	1375	99.99	0.162	0.161	0.1608	0.1795	0.1792	28.161

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
r_lrange_it	23.34
r_lrange_other	22.499
r_scangle_it	16.631
r_scangle_other	16.172
r_dihedral_angle_6_deg	15.073
r_dihedral_angle_3_deg	12.701
r_scbond_it	11.836
r_scbond_other	11.422
r_dihedral_angle_2_deg	9.383
r_mcangle_other	9.375
r_mcangle_it	9.364
r_dihedral_angle_1_deg	7.656
r_mcbond_it	6.652
r_mcbond_other	6.607
r_rigid_bond_restr	4.862
r_angle_refined_deg	1.977
r_angle_other_deg	0.839
r_xyhbond_nbd_refined	0.207
r_nbd_refined	0.178
r_symmetry_nbd_other	0.165
r_nbtor_refined	0.161
r_symmetry_nbd_refined	0.142
r_symmetry_xyhbond_nbd_refined	0.133
r_chiral_restr	0.107
r_nbd_other	0.098
r_symmetry_nbtor_other	0.073
r_symmetry_xyhbond_nbd_other	0.05
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	931
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	30

Software

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