2AGI

The leupeptin-trypsin covalent complex at 1.14 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AGE	PDB entry 2AGE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	ammonium sulfate, bis-tris propane, calcium chloride, benzamidine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.81	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.888	α = 90
b = 63.562	β = 90
c = 69.102	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	CCD	ADSC QUANTUM 4		2003-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.00000	ALS	8.3.1

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	1.14	46.63	99.64	0.04	0.04	13.1	3.2	88464	88464		-3

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	1.14	1.2			0.284	0.284	1.5	1.3	6920

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2AGE	1.14	46.63	88464	88464	4449	99.64	0.117	0.117	0.116	0.138	inherited from PDB entry 2AGE	12.663

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]
-0.06			-0.09		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.098
r_sphericity_free	16.976
r_dihedral_angle_4_deg	11.996
r_dihedral_angle_3_deg	10.309
r_sphericity_bonded	6.875
r_scangle_it	6.73
r_dihedral_angle_1_deg	6.677
r_scbond_it	5.283
r_mcangle_it	3.977
r_rigid_bond_restr	3.471
r_mcbond_it	3.083
r_mcbond_other	2.198
r_angle_other_deg	1.904
r_angle_refined_deg	1.869
r_nbd_refined	0.377
r_symmetry_vdw_other	0.356
r_nbd_other	0.27
r_symmetry_hbond_refined	0.229
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.137
r_metal_ion_refined	0.121
r_nbtor_other	0.102
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_bond_other_d	0.007
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1654
Nucleic Acid Atoms
Solvent Atoms	371
Heterogen Atoms	11

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
TRUNCATE	data reduction
EPMR	phasing
REFMAC	refinement
CCP4	data scaling
TRUNCATE	data scaling