6S1V | pdb_00006s1v

Crystal structure of dimeric M-PMV protease D26N mutant in complex with inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6S1U	6S1U, chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	292	Protein solution: 5.0 mg/mL protein with 1.4-fold molar excess (relative to dimeric protein) of Pro-0A1-Val-PSA-Ala-Met-Thr (inhibitor), 5 mM TCEP, 10 mM Tris buffer pH 7.4; Reservoir solution: 0.1 M sodium citrate buffer, 25% propan-2-ol, 5 mM TCEP;

Crystal Properties
Matthews coefficient	Solvent content
2.378	46.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.947	α = 90
b = 29.504	β = 101.71
c = 85.39	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 6M		2013-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	1.64	48.91	99.3	0.043	0.05	0.999	14.36	3.65		30408

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	1.64	1.74	98.3		0.826	0.97	0.568	1.37	3.56

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 (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	6S1U, chain A	1.64	48.91	29403	1004	99.29	0.18006	0.1787	0.19	0.22018	0.23	RANDOM	40.063

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]
1.35		-0.82	-0.76		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.882
r_dihedral_angle_3_deg	15.046
r_long_range_B_refined	8.846
r_long_range_B_other	8.831
r_dihedral_angle_1_deg	8.619
r_dihedral_angle_4_deg	8.397
r_scangle_other	5.247
r_mcangle_it	4.144
r_mcangle_other	4.142
r_scbond_it	3.463
r_scbond_other	3.454
r_mcbond_it	2.754
r_mcbond_other	2.749
r_angle_refined_deg	1.701
r_angle_other_deg	1.36
r_chiral_restr	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	1733
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms

Software

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