3ATM | pdb_00003atm

Crystal structure of trypsin complexed with 2-(1H-indol-3-yl)ethanamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A7T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.1M TRIS-HCL, 30% PEG 3350, 0.2M LITHIUM SULFATE, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.323	α = 90
b = 58.139	β = 90
c = 66.726	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	RIGAKU RAXIS IV			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	1.72	50	96.4	0.035	0.035	40.6	6.4	22247	22247		-3	13.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.72	1.78	90.8		0.077	0.077	18.5	6	2056

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)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3A7T	1.72	19.85	21090	21090	1113	99.8	0.15561	0.15561	0.15479	0.17	0.17141	0.17	RANDOM	9.571

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]
0.24			-0.14		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.157
r_dihedral_angle_4_deg	19.221
r_dihedral_angle_3_deg	11.114
r_dihedral_angle_1_deg	6.054
r_scangle_it	1.807
r_scbond_it	1.128
r_angle_refined_deg	1.071
r_angle_other_deg	0.789
r_mcangle_it	0.745
r_mcbond_it	0.504
r_symmetry_vdw_other	0.243
r_nbd_refined	0.231
r_symmetry_vdw_refined	0.226
r_nbd_other	0.186
r_nbtor_refined	0.171
r_symmetry_hbond_refined	0.163
r_xyhbond_nbd_refined	0.113
r_nbtor_other	0.083
r_mcbond_other	0.08
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1629
Nucleic Acid Atoms
Solvent Atoms	325
Heterogen Atoms	25

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling