9N3H | pdb_00009n3h

Crystal structure of HBV capsid with compound 18

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E0I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	13-18% (v/v) MPD, 280-310 mM trisodium citrate, and 100 mM Hepes pH 7.5. Protein:reservoir ratio of 2:1

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.152	α = 90
b = 88.152	β = 90
c = 290.557	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		2019-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.54	48.473	99.8	0.124	0.132	0.044	0.999	8.2	8.6		14719

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.54	2.66	99.4		0.921	0.982	0.336	0.924	1.9	8.3

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	MOLECULAR REPLACEMENT	FREE R-VALUE	2.543	48.473	14719	779	99.79	0.262	0.2605	0.2695	0.2966	0.2986	88.676

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]
-8.776	-4.388		-8.776		28.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.027
r_lrange_other	15.051
r_lrange_it	15.04
r_dihedral_angle_6_deg	14.665
r_mcangle_it	10.568
r_mcangle_other	10.568
r_scangle_it	10.196
r_scangle_other	10.193
r_dihedral_angle_1_deg	7.066
r_mcbond_it	6.59
r_mcbond_other	6.584
r_scbond_it	6.123
r_scbond_other	6.121
r_dihedral_angle_2_deg	5.008
r_angle_refined_deg	1.483
r_angle_other_deg	0.799
r_nbd_refined	0.251
r_xyhbond_nbd_refined	0.225
r_symmetry_nbd_other	0.221
r_nbd_other	0.21
r_nbtor_refined	0.194
r_symmetry_xyhbond_nbd_refined	0.168
r_symmetry_xyhbond_nbd_other	0.154
r_symmetry_nbd_refined	0.134
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.059
r_gen_planes_other	0.006
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2118
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	64

Software

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