6ZBP | pdb_00006zbp

H11-H4 complex with SARS-CoV-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YZ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Crystals were grown at using the sitting drop vapor diffusion method by mixing 0.2 uL of the 18 mg/mL H11-H4 RBD complex with 0.1 uL of the crystallization buffer containing 0.2 M Sodium acetate trihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 8000. The crystals grew overnight and were flash cooled in a solution containing the mother liquor with 30 % (v/v) ethylene glycol.

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.15	α = 90
b = 73.15	β = 90
c = 131.67	γ = 120

Symmetry
Space Group	P 31 2 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-F		2020-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97623	Diamond	I03

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	1.85	57.151	99.5	0.086	0.028	1	18.2	19.7		35506

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.9	99.5		2.05	0.46	0.7	1.7	20.9

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	6YZ5	1.85	57.151	35472	1808	99.733	0.187	0.185	0.19	0.2169	0.22	48.736

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]
2.091	1.046		2.091		-6.784

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.74
r_dihedral_angle_other_3_deg	24.12
r_dihedral_angle_1_deg	17.387
r_dihedral_angle_4_deg	16.664
r_dihedral_angle_3_deg	12.462
r_lrange_other	8.808
r_lrange_it	8.797
r_scangle_it	6.874
r_scangle_other	6.777
r_scbond_it	4.612
r_scbond_other	4.553
r_mcangle_it	3.896
r_mcangle_other	3.895
r_mcbond_it	3.014
r_mcbond_other	3.006
r_angle_refined_deg	1.682
r_angle_other_deg	1.405
r_symmetry_xyhbond_nbd_refined	0.233
r_nbd_refined	0.189
r_nbd_other	0.183
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.15
r_symmetry_nbd_refined	0.146
r_symmetry_nbtor_other	0.082
r_xyhbond_nbd_other	0.082
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2546
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	19

Software

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