6TM4 | pdb_00006tm4

NatL2 in complex with two molecules of salicylic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SIW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2M KSCN, 0.1 M sodium citrate pH 6, 24-32% PEG MME 2K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.46	α = 90
b = 139.24	β = 90
c = 129.66	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		2019-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.89	71.13	100	0.119	0.997	9.4	6.5		77807

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.89	1.94	100		1.628	0.65	1.3	6.7

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	6SIW	1.89	71.128	77773	3811	99.949	0.199	0.1978	0.21	0.2303	0.24	47.313

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]
-2.732			3.626		-0.894

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.437
r_dihedral_angle_4_deg	21.446
r_dihedral_angle_3_deg	14.626
r_dihedral_angle_1_deg	6.974
r_lrange_other	5.323
r_lrange_it	5.322
r_scangle_it	3.478
r_scangle_other	3.478
r_mcangle_it	2.734
r_mcangle_other	2.734
r_scbond_it	2.196
r_scbond_other	2.195
r_mcbond_it	1.795
r_mcbond_other	1.792
r_angle_refined_deg	1.563
r_angle_other_deg	1.306
r_nbd_other	0.218
r_symmetry_xyhbond_nbd_refined	0.205
r_nbd_refined	0.193
r_symmetry_nbd_other	0.18
r_symmetry_nbd_refined	0.18
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.147
r_ncsr_local_group_1	0.095
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.067
r_metal_ion_refined	0.056
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6727
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing