6Q9T | pdb_00006q9t

Protein-aromatic foldamer complex crystal structure

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KS3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	293	Ammonium sulfate 0.2 M, Sodium acetate 0.1 M pH 5.7, PEG 4000 14%, Sodium azide 3 mM

Crystal Properties
Matthews coefficient	Solvent content
2.52	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.3	α = 90
b = 80.96	β = 90
c = 45.62	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 EIGER X 9M	CRYOGENICALLY COOLED CHANNEL CUT CRYSTAL MONOCHROMATOR, CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS	2018-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980112	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.68	45.62	98.6	0.099	0.998	17.96	12.8		8622			72.25

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.68	2.84	91.3		0.99	0.859	2.02	12.64

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3KS3	2.68	45.62	8189	431	98.51	0.21732	0.2148	0.2193	0.26025	0.2629	RANDOM	69.834

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]
-4.59			-7.11		11.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.409
r_dihedral_angle_4_deg	19.909
r_dihedral_angle_3_deg	18.245
r_dihedral_angle_1_deg	9.292
r_long_range_B_refined	6.087
r_long_range_B_other	6.086
r_mcangle_other	4.434
r_mcangle_it	4.421
r_scangle_other	3.756
r_mcbond_other	2.653
r_mcbond_it	2.631
r_scbond_it	2.293
r_scbond_other	2.292
r_angle_refined_deg	2.009
r_angle_other_deg	1.551
r_chiral_restr	0.069
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.008
r_gen_planes_other	0.007
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1778
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	225

Software

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