8WD3 | pdb_00008wd3

The Crystal Structure of JMJD2A(M1-L359) from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OX0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2M KSCN, 0.1M Bis-Tris propane pH7.5, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2	38.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.641	α = 90
b = 97.111	β = 90
c = 141.083	γ = 90

Symmetry
Space Group	P 2 21 21

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 EIGER X 9M		2020-08-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.18057	CLSI	08B1-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.3	48.603	99.8	0.162	0.996	6.9	5.6		11222

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.3	3.56			0.675	0.867

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	3.3	48.603	11190	560	99.608	0.246	0.2439	0.25	0.2928	0.29	96.393

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]
10.332			-6.986		-3.346

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.962
r_dihedral_angle_6_deg	12.679
r_lrange_it	11.771
r_lrange_other	11.771
r_mcangle_it	6.518
r_mcangle_other	6.518
r_dihedral_angle_1_deg	6.384
r_scangle_it	5.898
r_scangle_other	5.898
r_mcbond_it	3.95
r_mcbond_other	3.949
r_dihedral_angle_2_deg	3.843
r_scbond_it	3.726
r_scbond_other	3.725
r_angle_refined_deg	1.025
r_angle_other_deg	0.336
r_symmetry_nbd_refined	0.314
r_nbd_other	0.249
r_nbd_refined	0.219
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.148
r_symmetry_nbtor_other	0.082
r_symmetry_xyhbond_nbd_other	0.057
r_symmetry_xyhbond_nbd_refined	0.05
r_chiral_restr	0.044
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5482
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	4

Software

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