3I06

Crystal structure of cruzain covalently bound to a purine nitrile

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	291	0.1 M Tris, 2.0 M NH4H2PO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.967	α = 90
b = 82.967	β = 90
c = 101.895	γ = 120

Symmetry
Space Group	P 65 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	100	CCD	ADSC QUANTUM 315r		2008-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.0	SSRL	BL7-1

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	1.1	41.48	92.7	0.052	0.052	8.399	11.6		77795

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	1.16	65.1		0.407	0.407	1.9	4.3	7781

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1ME3	1.1	41.48	77748	3940	92.52	0.12	0.119	0.142	RANDOM	10.649

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]
-0.32	-0.16		-0.32		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.311
r_dihedral_angle_4_deg	16.418
r_dihedral_angle_1_deg	12.638
r_sphericity_free	12.4
r_dihedral_angle_3_deg	10.632
r_sphericity_bonded	4.843
r_scangle_it	4.303
r_scbond_it	3.655
r_mcangle_it	2.61
r_mcbond_it	2.118
r_angle_refined_deg	2.016
r_rigid_bond_restr	1.804
r_angle_other_deg	1.546
r_mcbond_other	0.871
r_xyhbond_nbd_refined	0.383
r_nbd_refined	0.306
r_symmetry_vdw_other	0.274
r_symmetry_hbond_refined	0.251
r_symmetry_vdw_refined	0.246
r_nbd_other	0.204
r_nbtor_refined	0.184
r_chiral_restr	0.117
r_nbtor_other	0.094
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_gen_planes_other	0.01
r_bond_other_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1696
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	23

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction