9T2I | pdb_00009t2i

SP100 nuclear antigen with crystallization epitope mutations N816D:T820R

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277.15	0.2M ammonium sulfate 25% PEG3350 0.1M bis-tris pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.09	α = 90
b = 45.73	β = 102.37
c = 83.95	γ = 90

Symmetry
Space Group	C 1 2 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		2015-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

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	1.35	82	96	0.041	14.6	3.5		100552

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	1.36	1.4			1.006

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.35	56.191	100552	5030	95.496	0.16	0.1584	0.1584	0.1852	0.1853	RANDOM	29.848

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]
-0.07		0.183	-0.434		0.387

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	18.746
r_lrange_other	17.914
r_dihedral_angle_6_deg	15.353
r_scangle_it	13.835
r_scangle_other	13.832
r_dihedral_angle_3_deg	12.49
r_mcangle_it	10.351
r_mcangle_other	10.351
r_scbond_it	10.103
r_scbond_other	10.1
r_dihedral_angle_2_deg	9.791
r_mcbond_it	7.762
r_mcbond_other	7.736
r_dihedral_angle_1_deg	5.424
r_rigid_bond_restr	4.829
r_angle_refined_deg	1.783
r_angle_other_deg	0.696
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.219
r_nbd_other	0.2
r_nbtor_refined	0.175
r_symmetry_nbd_other	0.169
r_symmetry_nbd_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.139
r_ncsr_local_group_1	0.119
r_chiral_restr	0.118
r_metal_ion_refined	0.106
r_symmetry_nbtor_other	0.068
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2868
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	5

Software

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