3BPM

Crystal Structure of Falcipain-3 with Its inhibitor, Leupeptin

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	0.015 M Magnesium Acetate, 50 mM Sodium cacodylate, 1.3 M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.57	α = 90
b = 154.57	β = 90
c = 129.011	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 315	mirrors	2007-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.979	SSRL	BL9-1

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	2.5	92.85	100	0.091	0.023	27	15.9		20625

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	2.5	2.64	100		0.507	0.124	7.1	16.3

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3BPF	2.5	92.85	20625	19568	1056	99.98	0.19138	0.18959	0.22423	RANDOM	29.7

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]
-0.16	-0.08		-0.16		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.537
r_dihedral_angle_3_deg	16.086
r_dihedral_angle_4_deg	15.962
r_dihedral_angle_1_deg	6.715
r_scangle_it	2.259
r_angle_refined_deg	1.549
r_scbond_it	1.536
r_mcangle_it	0.937
r_angle_other_deg	0.91
r_mcbond_it	0.693
r_symmetry_vdw_other	0.241
r_nbd_refined	0.211
r_nbd_other	0.202
r_nbtor_refined	0.195
r_symmetry_hbond_refined	0.172
r_xyhbond_nbd_refined	0.153
r_mcbond_other	0.131
r_nbtor_other	0.095
r_symmetry_vdw_refined	0.089
r_chiral_restr	0.086
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3815
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing