4JYT

Crystal Structure of Matriptase 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	1EAX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.3	291	0.1M Tris, 0.2M MgCl2, 20% PEG8000 , pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.423	α = 90
b = 140.658	β = 90
c = 51.325	γ = 90

Symmetry
Space Group	C 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++	Mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2	30	92.5	0.057	11.7	2.2	33649	15425

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	95.3		0.186	2.6	1.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1EAX	2	25.91	14647	777	92.46	0.21742	0.21583	0.24755	RANDOM	15.854

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]
-0.08			-0.03		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.073
r_dihedral_angle_4_deg	17.579
r_dihedral_angle_3_deg	12.475
r_dihedral_angle_1_deg	6.688
r_scangle_it	2.362
r_scbond_it	1.711
r_angle_refined_deg	1.477
r_mcangle_it	0.936
r_angle_other_deg	0.775
r_mcbond_it	0.754
r_symmetry_vdw_other	0.282
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.212
r_symmetry_hbond_refined	0.206
r_nbd_other	0.2
r_xyhbond_nbd_refined	0.147
r_mcbond_other	0.132
r_nbtor_other	0.084
r_chiral_restr	0.078
r_xyhbond_nbd_other	0.024
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbtor_refined
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1858
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	40

Software

Software
Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling