6TCX | pdb_00006tcx

Papain bound to a natural cysteine protease inhibitor from Streptomyces mobaraensis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9PAP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	100 mM HEPES pH 7.5 and 80% 2-Methyl-2,4-pentanediol (MPD)

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.644	α = 90
b = 48.921	β = 90
c = 101.547	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 PILATUS 6M		2018-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97242	ESRF	ID23-1

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	1.65	50.65	99.8	0.026	0.999	15.1	13.1		26295

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	1.65	1.68			0.252	0.876

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	9PAP	1.65	44.112	26239	1325	99.749	0.198	0.1964	0.21	0.2214	0.23	24.649

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]
-0.312			1.251		-0.939

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.326
r_dihedral_angle_4_deg	15.895
r_dihedral_angle_other_3_deg	12.97
r_dihedral_angle_3_deg	10.435
r_dihedral_angle_1_deg	6.009
r_lrange_other	3.28
r_lrange_it	3.277
r_scangle_it	2.028
r_scangle_other	2.027
r_mcangle_other	1.503
r_mcangle_it	1.501
r_scbond_it	1.258
r_scbond_other	1.258
r_angle_other_deg	1.207
r_angle_refined_deg	1.175
r_mcbond_it	0.912
r_mcbond_other	0.907
r_nbd_other	0.188
r_nbd_refined	0.173
r_nbtor_refined	0.166
r_symmetry_nbd_other	0.165
r_symmetry_xyhbond_nbd_refined	0.135
r_xyhbond_nbd_refined	0.103
r_symmetry_nbtor_other	0.073
r_symmetry_nbd_refined	0.067
r_chiral_restr	0.05
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1636
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
autoXDS	data reduction
Aimless	data scaling
MOLREP	phasing