7NRA | pdb_00007nra

The structure of the SBP TarP_Sse in complex with cinnamate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7NR2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	290	1.6 M tri-sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.12	α = 90
b = 70.2	β = 93.12
c = 85.01	γ = 90

Symmetry
Space Group	P 1 21 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		2014-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9500	Diamond	I03

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	1.91	64.02	98.6	0.092	0.079	9.9	3.2		57762

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	1.91	1.96	99.8		0.559	0.41	2.1	3.3

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	7NR2	1.91	64.02	57745	2852	98.499	0.203	0.2001	0.21	0.2608	0.27	30.818

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]
-1.606		0.697	-1.28		2.793

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.387
r_scbond_other	30.107
r_scbond_it	30.104
r_mcbond_it	26.186
r_mcbond_other	26.076
r_lrange_it	25.039
r_lrange_other	25.037
r_scangle_other	24.941
r_scangle_it	24.94
r_mcangle_other	21.818
r_mcangle_it	21.789
r_dihedral_angle_4_deg	18.995
r_dihedral_angle_3_deg	14.293
r_dihedral_angle_1_deg	7.12
r_angle_refined_deg	1.509
r_angle_other_deg	1.315
r_nbd_other	0.229
r_symmetry_xyhbond_nbd_refined	0.225
r_symmetry_nbd_refined	0.221
r_nbd_refined	0.203
r_symmetry_nbd_other	0.173
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_other	0.082
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.072
r_gen_planes_other	0.011
r_gen_planes_refined	0.01
r_bond_refined_d	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5015
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	22

Software

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