9GP1 | pdb_00009gp1

Jumonji domain-containing protein 2A with crystallization epitope mutatios K330R:A334E

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GD4

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.03	α = 90
b = 101.6	β = 99.38
c = 141.43	γ = 90

Symmetry
Space Group	P 1 21 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	2.21	101.6	97.8	0.993	11.7	3.4		77812

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	2.21	2.27			0.606

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	2.21	82.135	77788	3949	97.613	0.217	0.215	0.215	0.2589	0.259	42.601

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]
-0.098		-0.303	-0.862		1.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.3
r_dihedral_angle_6_deg	14.508
r_lrange_it	10.106
r_scangle_it	7.675
r_dihedral_angle_2_deg	7.302
r_dihedral_angle_1_deg	7.015
r_mcangle_it	6.938
r_scbond_it	5.491
r_mcbond_it	4.814
r_angle_refined_deg	1.757
r_symmetry_nbd_refined	0.352
r_nbtor_refined	0.316
r_symmetry_xyhbond_nbd_refined	0.246
r_metal_ion_refined	0.237
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.205
r_chiral_restr	0.129
r_ncsr_local_group_2	0.083
r_ncsr_local_group_3	0.082
r_ncsr_local_group_5	0.08
r_ncsr_local_group_1	0.075
r_ncsr_local_group_4	0.075
r_ncsr_local_group_6	0.059
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11115
Nucleic Acid Atoms
Solvent Atoms	537
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing