7WNS | pdb_00007wns

Crystal structure of ENF peptide binding protein from Silkworm

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	289	O.5M magnesium formate, 0.1M Bis-Tris pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
4.22	70.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.477	α = 90
b = 121.692	β = 90
c = 253.769	γ = 90

Symmetry
Space Group	C 2 2 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 PILATUS3 6M		2018-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.799	50	99.5	0.082	0.082	36.67	13.2		78393

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	1.8	1.83	99		0.928	3	12.8

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	SAD	THROUGHOUT	1.799	35.543	78178	3936	99.279	0.174	0.1733	0.18	0.1853	0.2	RANDOM	28.324

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]
0.004			-0.106		0.103

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.148
r_dihedral_angle_4_deg	16.223
r_dihedral_angle_3_deg	13.474
r_lrange_it	8.44
r_lrange_other	8.265
r_dihedral_angle_1_deg	7.366
r_scangle_it	6.405
r_scangle_other	6.404
r_mcangle_it	4.84
r_mcangle_other	4.84
r_scbond_it	4.244
r_scbond_other	4.243
r_mcbond_it	3.679
r_mcbond_other	3.672
r_angle_other_deg	2.41
r_angle_refined_deg	1.997
r_symmetry_nbd_refined	0.232
r_nbd_other	0.225
r_symmetry_nbd_other	0.216
r_nbd_refined	0.208
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.173
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.109
r_symmetry_nbtor_other	0.081
r_bond_other_d	0.035
r_gen_planes_other	0.018
r_bond_refined_d	0.017
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3434
Nucleic Acid Atoms
Solvent Atoms	456
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALA	data scaling
AutoSol	phasing