3M7Q | pdb_00003m7q

Crystal structure of recombinant Kunitz Type serine protease Inhibitor-1 from the Caribbean sea anemone stichodactyla helianthus in complex with bovine pancreatic trypsin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SHI	PDB entry 1SHI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	288.15	25% PEG 3350, 0.2M magnesium chloride hexahydrate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288.15K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.279	α = 90
b = 66.551	β = 90
c = 70.937	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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	1.5	EMBL/DESY, HAMBURG	X13

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	1.7	50		0.065	26.5	5.8		30937			14.6

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	1.7	1.73	97.8		0.217	9	5.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	PDB entry 1SHI	1.7	30	2	30937	1540	98.79	0.15938	0.15778	0.16	0.18847	0.19	RANDOM	14.589

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]
0.11			0.26		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.188
r_dihedral_angle_4_deg	13.69
r_dihedral_angle_3_deg	11.188
r_dihedral_angle_1_deg	5.442
r_scangle_it	1.994
r_mcangle_it	1.469
r_scbond_it	1.323
r_mcbond_it	1.033
r_angle_refined_deg	0.955
r_nbtor_refined	0.292

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.188
r_dihedral_angle_4_deg	13.69
r_dihedral_angle_3_deg	11.188
r_dihedral_angle_1_deg	5.442
r_scangle_it	1.994
r_mcangle_it	1.469
r_scbond_it	1.323
r_mcbond_it	1.033
r_angle_refined_deg	0.955
r_nbtor_refined	0.292
r_nbd_refined	0.169
r_symmetry_vdw_refined	0.14
r_symmetry_hbond_refined	0.115
r_xyhbond_nbd_refined	0.091
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2095
Nucleic Acid Atoms
Solvent Atoms	526
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.