9GLE

Jumonji domain-containing protein 2A with crystallization epitope mutations A91T:T93S

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OQ6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M lithium sulfate, 25% PEG3350, 0.1M bis-tris pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.7	α = 90
b = 90.78	β = 107.19
c = 90.67	γ = 90

Symmetry
Space Group	C 1 2 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 6M		2014-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

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	1.88	40.449	99.5	0.997	12.5	3.4		73694

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	1.88	1.93			0.783

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	1.88	40.449	73693	3667	99.447	0.187	0.1854	0.1854	0.2223	0.2224	39.163

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]
1.908		0.588	1.152		-2.873

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.517
r_dihedral_angle_3_deg	13.594
r_dihedral_angle_2_deg	8.906
r_lrange_other	8.859
r_lrange_it	8.858
r_scangle_it	7.379
r_scangle_other	7.378
r_dihedral_angle_1_deg	7.08
r_mcangle_it	6.1
r_mcangle_other	6.1
r_scbond_it	5.403
r_scbond_other	5.402
r_mcbond_other	4.844
r_mcbond_it	4.843
r_angle_refined_deg	2.053
r_angle_other_deg	0.863
r_symmetry_xyhbond_nbd_refined	0.685
r_symmetry_nbd_refined	0.584
r_metal_ion_refined	0.269
r_xyhbond_nbd_other	0.23
r_nbd_refined	0.208
r_nbtor_refined	0.183
r_nbd_other	0.183
r_symmetry_nbd_other	0.167
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.114
r_ncsr_local_group_1	0.101
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.03
r_bond_refined_d	0.012
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5498
Nucleic Acid Atoms
Solvent Atoms	446
Heterogen Atoms	53

Software

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