3GY4 | pdb_00003gy4

A comparative study on the inhibition of bovine beta-trypsin by bis-benzamidines diminazene and pentamidine by X-ray crystallography and ITC

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	14% PEG8000, 0.1M ammonium sulfate, 0.05M Tris-HCl, 0.008M CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.265	α = 90
b = 58.106	β = 90
c = 66.766	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	IMAGE PLATE	MAR scanner 345 mm plate		2006-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU ULTRAX 18	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.55	25	97.6	0.037	29.21	3.3	31378	30624	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.55	1.59	97		0.122	8.9	3.1	1991

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	1.55	25	1	31303	29342	1253	97.7	0.15629	0.15547	0.15	0.17539	0.17	RANDOM	10.858

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]
-0.07			-0.22		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.235
r_dihedral_angle_4_deg	14.621
r_dihedral_angle_3_deg	12.118
r_dihedral_angle_1_deg	5.901
r_scangle_it	2.417
r_scbond_it	1.645
r_angle_refined_deg	1.16
r_mcangle_it	0.954
r_mcbond_it	0.626
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.235
r_dihedral_angle_4_deg	14.621
r_dihedral_angle_3_deg	12.118
r_dihedral_angle_1_deg	5.901
r_scangle_it	2.417
r_scbond_it	1.645
r_angle_refined_deg	1.16
r_mcangle_it	0.954
r_mcbond_it	0.626
r_nbtor_refined	0.303
r_nbd_refined	0.263
r_symmetry_vdw_refined	0.214
r_metal_ion_refined	0.128
r_symmetry_hbond_refined	0.119
r_xyhbond_nbd_refined	0.11
r_chiral_restr	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1629
Nucleic Acid Atoms
Solvent Atoms	365
Heterogen Atoms	61

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.