6TVQ | pdb_00006tvq

Structure of native gp41 derived peptide fusion inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	292.15	Ammonium sulfate, PEG 3350, Bis-Tris

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.875	α = 90
b = 44.875	β = 90
c = 209.645	γ = 120

Symmetry
Space Group	H 3 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 PILATUS3 S 6M		2019-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918400	BESSY	14.1

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	1.45	38.241	100	0.152	0.048	0.997	8	11.1		14982

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.48			0.669	0.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	AB INITIO PHASING	FREE R-VALUE	1.45	38.24	14980	710	99.953	0.19	0.1879	0.2	0.2426	0.25	27.725

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]
1.856	0.928		1.856		-6.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.128
r_dihedral_angle_4_deg	15.095
r_dihedral_angle_3_deg	13.986
r_scangle_it	6.362
r_scangle_other	6.355
r_lrange_it	5.616
r_dihedral_angle_1_deg	5.355
r_scbond_it	5.329
r_scbond_other	5.303
r_lrange_other	5.247
r_mcangle_it	5.023
r_mcangle_other	5.016
r_mcbond_it	4.138
r_mcbond_other	4.132
r_rigid_bond_restr	4.109
r_angle_refined_deg	1.71
r_angle_other_deg	1.585
r_xyhbond_nbd_refined	0.311
r_symmetry_nbd_refined	0.253
r_nbd_refined	0.218
r_nbd_other	0.183
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.133
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	535
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
ACORN	phasing