7D4A | pdb_00007d4a

The Crystal Structure of human JMJD2A Tudor domain from Biortus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GF7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M NaCl, 0.1M HEPES pH7.5, 1.6M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
3.42	63.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.11	α = 90
b = 135.11	β = 90
c = 135.11	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 PILATUS3 6M		2020-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.976253	ESRF	ID30B

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	2.2	67.56	99.9	0.129	21.4	41.4		11007

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	2.2	2.26			2.749

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	2gf7	2.201	55.219	10991	558	99.918	0.232	0.2297	0.24	0.2722	0.28	52.144

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_dihedral_angle_2_deg	35.976
r_dihedral_angle_3_deg	14.457
r_dihedral_angle_1_deg	7.569
r_lrange_it	6.89
r_lrange_other	6.872
r_dihedral_angle_4_deg	6.616
r_scangle_it	5.267
r_scangle_other	5.25
r_mcangle_other	3.698
r_mcangle_it	3.68
r_scbond_it	3.211
r_scbond_other	3.185
r_mcbond_it	2.435
r_mcbond_other	2.392
r_angle_refined_deg	1.255
r_angle_other_deg	1.197
r_nbd_other	0.19
r_symmetry_nbd_other	0.181
r_nbd_refined	0.177
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.123
r_symmetry_xyhbond_nbd_refined	0.081
r_symmetry_nbtor_other	0.073
r_symmetry_nbd_refined	0.052
r_chiral_restr	0.046
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	930
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	5

Software

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