8WUG

The Crystal Structure of JMJD2D from Biortus.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M HEPES, NaOH pH 7.5, 2% PEG 400, 2M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.34	α = 90
b = 71.34	β = 90
c = 150.873	γ = 90

Symmetry
Space Group	P 43 21 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 PILATUS3 6M		2023-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.978530	SSRF	BL19U1

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	1.7	47.89	92	0.029	60.6	15.9		40301

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	1.7	1.74			0.162	13.4

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	1.7	47.887	40220	2006	92.009	0.163	0.1612	0.1876	19.554

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]
0.597			0.597		-1.193

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.821
r_dihedral_angle_3_deg	12.19
r_dihedral_angle_1_deg	6.476
r_dihedral_angle_2_deg	6.231
r_lrange_it	5.695
r_lrange_other	5.38
r_scangle_it	2.958
r_scangle_other	2.958
r_mcangle_it	1.896
r_mcangle_other	1.896
r_scbond_it	1.889
r_scbond_other	1.888
r_mcbond_it	1.184
r_mcbond_other	1.184
r_angle_refined_deg	1.131
r_angle_other_deg	0.399
r_nbd_refined	0.211
r_nbtor_refined	0.185
r_symmetry_nbd_other	0.184
r_symmetry_xyhbond_nbd_refined	0.169
r_xyhbond_nbd_refined	0.159
r_symmetry_nbd_refined	0.117
r_nbd_other	0.107
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.059
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2687
Nucleic Acid Atoms
Solvent Atoms	421
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing