7NTD | pdb_00007ntd

The structure of the SBP TarP_Csal in complex with ferulate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7NSW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	290	0.2 M MgCl2, 0.1 M Tris pH 8.5 and 20 % (w/v) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.86	α = 101.68
b = 52.28	β = 98.59
c = 68.53	γ = 104.9

Symmetry
Space Group	P 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		2015-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97949	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.75	48.89	96.8	0.08	0.073	0.988	6.2	2		62516

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.8	95.4		0.687	0.62	0.47		2

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	7NSW	1.75	47.124	62507	3047	96.822	0.194	0.1912	0.2	0.2517	0.26	33.081

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]
-1.778	-0.73	0.443	0.895	0.543	0.474

RMS Deviations
Key	Refinement Restraint Deviation
r_scbond_it	32.707
r_scbond_other	32.706
r_dihedral_angle_2_deg	30.665
r_scangle_it	24.544
r_scangle_other	24.504
r_lrange_it	23.341
r_lrange_other	23.339
r_dihedral_angle_4_deg	16.312
r_mcbond_it	15.085
r_mcbond_other	15.069
r_mcangle_it	14.338
r_mcangle_other	14.336
r_dihedral_angle_3_deg	14.045
r_dihedral_angle_1_deg	6.647
r_angle_refined_deg	1.458
r_angle_other_deg	1.328
r_symmetry_nbd_refined	0.205
r_nbd_refined	0.199
r_nbd_other	0.188
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.142
r_metal_ion_refined	0.101
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_symmetry_xyhbond_nbd_other	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5006
Nucleic Acid Atoms
Solvent Atoms	472
Heterogen Atoms	35

Software

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