9HAJ | pdb_00009haj

Structure of compound 1 bound to SARS-CoV-2 main protease

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Internal structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	Morpheus B3

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.046	α = 90
b = 99.654	β = 90
c = 104.145	γ = 90

Symmetry
Space Group	P 21 21 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 EIGER2 X 16M		2022-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00	SLS	X06DA

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	1.276	57.03	99.8	0.136	0.048	0.997	8.2	6		183140

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	1.276	1.299	98.1		2.77	1.01	0.371	0.7

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	1.276	57.03	182872	9101	99.593	0.165	0.164	0.1747	0.1918	0.1976	16.904

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]
-0.358			-0.187		0.546

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.846
r_dihedral_angle_3_deg	10.779
r_lrange_it	10.46
r_lrange_other	8.98
r_dihedral_angle_2_deg	6.968
r_dihedral_angle_1_deg	6.866
r_scangle_it	5.683
r_scangle_other	5.682
r_mcangle_other	4.43
r_mcangle_it	4.429
r_scbond_it	3.765
r_scbond_other	3.764
r_mcbond_it	2.867
r_mcbond_other	2.856
r_rigid_bond_restr	2.251
r_angle_refined_deg	1.489
r_angle_other_deg	0.532
r_nbd_refined	0.209
r_nbd_other	0.2
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.181
r_symmetry_nbd_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.169
r_ncsr_local_group_1	0.122
r_xyhbond_nbd_refined	0.113
r_xyhbond_nbd_other	0.099
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.076
r_gen_planes_refined	0.007
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4696
Nucleic Acid Atoms
Solvent Atoms	644
Heterogen Atoms	67

Software

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