2AYW | pdb_00002ayw

Crystal Structure of the complex formed between trypsin and a designed synthetic highly potent inhibitor in the presence of benzamidine at 0.97 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	290	5mM MES, 1mM CaCl2, 2.5mM benzamidine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.1	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.55	α = 90
b = 68.55	β = 90
c = 73.33	γ = 120

Symmetry
Space Group	P 32 2 1

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	MARRESEARCH	Mirror	2000-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.91	EMBL/DESY, HAMBURG	BW7B

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	0.97	20	99.6	0.065	18.2		225251	116664			7.66

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	0.97	1	95.5		0.401	3.1

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	1JRT	0.97	20	116664	114997	1167	99.6	0.13773	0.13773	0.13355	0.1426	0.15683	0.1635	RANDOM	9.672

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]
-0.15	-0.08		-0.15		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.973
r_dihedral_angle_4_deg	18.526
r_dihedral_angle_3_deg	13.236
r_dihedral_angle_1_deg	6.727
r_sphericity_free	5.517
r_scangle_it	3.27
r_scbond_it	3.038
r_angle_other_deg	2.908
r_sphericity_bonded	2.546
r_rigid_bond_restr	1.945
r_mcangle_it	1.794
r_angle_refined_deg	1.66
r_mcbond_it	1.284
r_mcbond_other	0.548
r_symmetry_vdw_other	0.281
r_symmetry_vdw_refined	0.244
r_symmetry_hbond_refined	0.243
r_nbd_refined	0.206
r_nbd_other	0.191
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.182
r_chiral_restr	0.104
r_metal_ion_refined	0.097
r_nbtor_other	0.094
r_gen_planes_refined	0.019
r_bond_refined_d	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1629
Nucleic Acid Atoms
Solvent Atoms	449
Heterogen Atoms	105

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
AMoRE	phasing