9RHT | pdb_00009rht

Structure of 3CL protease with a bound inhibitor

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		In-house structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	30mM sodium nitrate, 30mM disodium hydrogen phosphate, 30mM ammonium sulfate, 100mM MES imidazole pH 6.5, 20%(w/v) PEG 550 MME, 10%(w/v) PEG 20K (Morpheus condition C1)

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.78	α = 90
b = 99.41	β = 90
c = 103.98	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 EIGER X 16M		2022-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.624	71.8	91.7	0.062	1	13	13.4		67317

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.624	1.759			0.582	0.341	1.7

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	1.624	56.846	67317	3504	75.392	0.194	0.1919	0.1919	0.2256	0.2256	21.442

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]
-0.005			-0.01		0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.795
r_dihedral_angle_3_deg	15.363
r_dihedral_angle_2_deg	7.257
r_dihedral_angle_1_deg	7.255
r_lrange_it	7.229
r_lrange_other	7.102
r_scangle_it	5.267
r_scangle_other	5.266
r_scbond_it	3.364
r_scbond_other	3.363
r_mcangle_it	3.173
r_mcangle_other	3.173
r_mcbond_it	2.145
r_mcbond_other	2.138
r_angle_refined_deg	1.505
r_angle_other_deg	0.518
r_symmetry_nbd_refined	0.246
r_nbd_refined	0.223
r_symmetry_xyhbond_nbd_refined	0.219
r_nbd_other	0.206
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.179
r_metal_ion_refined	0.17
r_ncsr_local_group_1	0.116
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.078
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4687
Nucleic Acid Atoms
Solvent Atoms	502
Heterogen Atoms	51

Software

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