9H44 | pdb_00009h44

Jumonji domain-containing protein 2B with crown ether and crystallization epitope mutations L916G:R917A:A918D

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	Hampton Index well B7 0.056 M sodium phosphate monobasic 1.344 M potassium phosphate dibasic

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.93	α = 90
b = 87.93	β = 90
c = 142.91	γ = 120

Symmetry
Space Group	H 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		2016-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

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	1.74	32.31	99.3	0.053	20.5	8.7		21921

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	1.74	1.79			0.746

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	1.74	32.308	21920	1107	99.257	0.204	0.203	0.2029	0.2251	0.2249	39.68

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]
0.007	0.003		0.007		-0.021

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.02
r_lrange_it	13.35
r_dihedral_angle_3_deg	12.026
r_scangle_it	7.609
r_dihedral_angle_2_deg	7.558
r_dihedral_angle_1_deg	6.632
r_scbond_it	5.512
r_mcangle_it	4.94
r_mcbond_it	3.869
r_angle_refined_deg	2.048

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.02
r_lrange_it	13.35
r_dihedral_angle_3_deg	12.026
r_scangle_it	7.609
r_dihedral_angle_2_deg	7.558
r_dihedral_angle_1_deg	6.632
r_scbond_it	5.512
r_mcangle_it	4.94
r_mcbond_it	3.869
r_angle_refined_deg	2.048
r_symmetry_nbd_refined	0.636
r_symmetry_xyhbond_nbd_refined	0.383
r_nbtor_refined	0.318
r_nbd_refined	0.282
r_xyhbond_nbd_refined	0.227
r_chiral_restr	0.147
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1010
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	19

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.