3BPF | pdb_00003bpf

Crystal Structure of Falcipain-2 with Its inhibitor, E64

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	100 mM Sodium Citrate, 10% PEG 3350, 100 mM Magnesium Formate, 5% Glycerol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.93	75.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.778	α = 90
b = 167.81	β = 90
c = 177.758	γ = 90

Symmetry
Space Group	C 2 2 21

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	2006-03-08	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 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	2.83	66.7	99.3	0.201	10.04	7.3		45440		3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.83	2.99	96.5		0.653	1.22	7.04

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1YVB	2.9	66.67	45440	2418	99.9	0.27794	0.27546	0.28	0.32542	0.32	RANDOM	66.289

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]
0.58			-1.22		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.34
r_dihedral_angle_3_deg	15.389
r_dihedral_angle_4_deg	10.928
r_dihedral_angle_1_deg	6.458
r_angle_refined_deg	1.049
r_angle_other_deg	0.812
r_scangle_it	0.709
r_scbond_it	0.54
r_mcangle_it	0.419
r_mcbond_it	0.358
r_nbd_refined	0.205
r_nbtor_refined	0.184
r_nbd_other	0.177
r_symmetry_vdw_other	0.174
r_xyhbond_nbd_refined	0.167
r_symmetry_vdw_refined	0.145
r_symmetry_hbond_refined	0.134
r_xyhbond_nbd_other	0.086
r_nbtor_other	0.084
r_chiral_restr	0.062
r_mcbond_other	0.035
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	7305
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	106

Software

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