7NSW | pdb_00007nsw

The structure of the SBP TarP_Csal in complex with coumarate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	290	0.2 M MgCl2, 0.1 M Hepes pH 7.0 and 25 % (w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.17	α = 90
b = 119.94	β = 90
c = 62.04	γ = 90

Symmetry
Space Group	P 21 21 2

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		2015-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91731	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.67	34.25	99.6	0.114	0.049	9.8	7.1		71530

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.67	1.71	99.4		1.145	0.56	1.4	6.1

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	7NRR	1.67	34.25	71488	3434	99.48	0.2	0.1973	0.21	0.2512	0.21	25.282

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]
3.303			-1.933		-1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.476
r_scbond_it	21.789
r_scbond_other	21.785
r_scangle_it	18.288
r_scangle_other	18.286
r_dihedral_angle_4_deg	16.324
r_lrange_it	16.137
r_lrange_other	16.136
r_dihedral_angle_3_deg	13.922
r_mcbond_it	7.996
r_mcbond_other	7.985
r_mcangle_other	7.732
r_mcangle_it	7.731
r_dihedral_angle_1_deg	6.569
r_angle_refined_deg	1.643
r_angle_other_deg	1.456
r_symmetry_nbd_refined	0.243
r_nbd_other	0.213
r_nbd_refined	0.207
r_symmetry_nbd_other	0.18
r_symmetry_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.152
r_metal_ion_refined	0.099
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.01
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	5101
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	31

Software

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