1ZDP | pdb_00001zdp

Crystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-thiorphan

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TLN	PDB ENTRY 3TLN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	dilution with H2O	7.2	277	Tris acetate, calcium acetate, DMSO, pH 7.20, dilution with H2O, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94	α = 90
b = 94	β = 90
c = 132.1	γ = 120

Symmetry
Space Group	P 61 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	298	FILM	KODAK	GRAPHITE MONOCHROMATOR, COLLIMATING SLITS	1987-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ELLIOTT GX-21	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.7	30	68	0.098	0.038		2.1		26142			14.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	NONE	PDB ENTRY 3TLN	1.7	10	25988	25988		68	0.183	0.183	0.183	0.17

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]

RMS Deviations
Key	Refinement Restraint Deviation
t_dihedral_angle_d	16.712
t_it	4.228
t_angle_deg	3.53
t_nbd	0.062
t_bond_d	0.02
t_gen_planes	0.015
t_trig_c_planes	0.013
t_incorr_chiral_ct

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2432
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	22

Software

Software
Software Name	Purpose
OSCTST	data collection
ROTAVATA	data reduction
TNT	refinement
OSCTST	data reduction
CCP4	data scaling
ROTAVATA	data scaling
TNT	phasing

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.