8OW4 | pdb_00008ow4

2.75 angstrom crystal structure of human NFAT1 with bound DNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OWR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	0.1 M sodium cacodylate pH 6.0, 8% w/v PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.497	α = 90
b = 94.426	β = 93.568
c = 129.449	γ = 90

Symmetry
Space Group	I 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		2022-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.979181	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.75	82.242	97.3	0.067	0.088	0.056	0.996	10.5	4.3		30970

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.88	99.9		0.506	0.665	0.427	0.863	2.1	4.3

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	2.75	82.242	30966	1717	97.228	0.219	0.2159	0.22	0.2728	0.27	RANDOM	84.321

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]
4.826		6.151	-3.875		-1.705

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.182
r_dihedral_angle_3_deg	19.053
r_dihedral_angle_6_deg	14.291
r_lrange_it	10.832
r_lrange_other	10.832
r_dihedral_angle_1_deg	9.033
r_scangle_it	8.377
r_scangle_other	8.376
r_mcangle_it	8.129
r_mcangle_other	8.128
r_scbond_it	5.933
r_scbond_other	5.932
r_mcbond_it	5.499
r_mcbond_other	5.497
r_angle_refined_deg	1.835
r_angle_other_deg	0.498
r_nbd_other	0.437
r_symmetry_nbd_refined	0.244
r_symmetry_xyhbond_nbd_refined	0.236
r_symmetry_nbd_other	0.213
r_nbd_refined	0.198
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.189
r_ncsr_local_group_1	0.109
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.089
r_ncsr_local_group_2	0.081
r_ncsr_local_group_3	0.066
r_symmetry_xyhbond_nbd_other	0.04
r_chiral_restr_other	0.009
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4027
Nucleic Acid Atoms	1218
Solvent Atoms	9
Heterogen Atoms

Software

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