7HUD | pdb_00007hud

PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment B08 from the F2X-Entry Screen in monoclinic space group

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y2E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.7	291	0.2 M MIB (sodium malonate, imidazole, and boric acid in the molar ratios 2:3:3) pH 7.7, 23.5 % PEG 1500, 5 % DMSO, 1 mM DTT. Crystal seeds were used to ensure reproducible crystal growth.

Crystal Properties
Matthews coefficient	Solvent content
1.9	35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.55	α = 90
b = 52.81	β = 102.65
c = 44.69	γ = 90

Symmetry
Space Group	C 1 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 PILATUS3 2M		2022-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.61	47.64	99.6	0.087	0.096	0.9990000000000001	12.16			33149

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.61	1.71		99.2	1.768	1.9409999999999998	0.363

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.61	47.64	31490	1658	99.65	0.2006	0.19908	0.2066	0.22864	0.2352	RANDOM	27.876

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]
1.63		-0.86	-0.18		-0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.107
r_dihedral_angle_3_deg	14.807
r_dihedral_angle_4_deg	12.542
r_dihedral_angle_1_deg	7.779
r_long_range_B_other	6.21
r_long_range_B_refined	6.209
r_scangle_other	4.793
r_mcangle_it	3.162
r_mcangle_other	3.162
r_scbond_it	3.094
r_scbond_other	3.093
r_mcbond_it	2.235
r_mcbond_other	2.234
r_angle_refined_deg	1.527
r_angle_other_deg	1.406
r_chiral_restr	0.076
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2367
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	22

Software

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