6NTT | pdb_00006ntt

X-ray Crystal Structure of Soybean Trypsin Inhibitor (Kunitz) Complexed with 1,5-Disulfonyl Naphthalene

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	Lyophilized protein dissolved in water to 25 mg/ml. Sitting drop vapor diffusion against reservoirs of 25% PEG 3350 with 0.10 M MES buffer ph 6.5. 3 ul drops composed of equal amounts of protein stock solution and reservoir supplemented with 0.10 M 1,5-Disulfonyl Naphthalene. Crystallization time about 2 weeks.

Crystal Properties
Matthews coefficient	Solvent content
2.23	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.88	α = 90
b = 64.68	β = 97.52
c = 69.08	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	173	CCD	MAR CCD 130 mm		2012-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.0	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.4	32.61	99	0.122	0.124	0.136	0.99	4.7	4.7		13649			83

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.45	85		0.481	0.538	2.2	4.5

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	1AVU	2.4	32.61	12813	656	93.2	0.21376	0.20924	0.21	0.30595	0.32	RANDOM	68.999

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]
-1.29		-2.2	-1.71		3.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.46
r_dihedral_angle_4_deg	17.478
r_dihedral_angle_3_deg	15.304
r_dihedral_angle_1_deg	8.191
r_long_range_B_refined	6.946
r_long_range_B_other	6.946
r_scangle_other	3.731
r_mcangle_it	3.302
r_mcangle_other	3.302
r_scbond_it	2.284
r_scbond_other	2.283
r_mcbond_it	2.074
r_mcbond_other	2.074
r_angle_refined_deg	1.284
r_angle_other_deg	1.1
r_chiral_restr	0.049
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d
r_gen_planes_other
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	2739
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	90

Software

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