2P7U | pdb_00002p7u

The crystal structure of rhodesain, the major cysteine protease of T. brucei rhodesiense, bound to inhibitor K777

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F2A	1F2A WITHOUT INHIBITOR OR WATERS, WITH SIDE CHAINS THAT DIFFER CUT BACK TO ALANINE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	1.0 M Sodium citrate; imidazole pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.377	α = 120.38
b = 39.716	β = 93.89
c = 39.566	γ = 101.18

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2000-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.65	30	89.7	0.047		1.8		18751

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)
	1.65	1.7	83.7		0.147

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1F2A WITHOUT INHIBITOR OR WATERS, WITH SIDE CHAINS THAT DIFFER CUT BACK TO ALANINE	1.65	19.46	51956	17747	950	89.47	0.137	0.135	0.14	0.175	0.18	RANDOM	13.33

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]
0.26	0.17	0.51	-0.41	0.28	0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.843
r_dihedral_angle_4_deg	20.611
r_dihedral_angle_3_deg	12.812
r_dihedral_angle_1_deg	5.671
r_scangle_it	4.593
r_scbond_it	3.17
r_mcangle_it	1.904
r_angle_refined_deg	1.673
r_angle_other_deg	1.665
r_mcbond_it	1.543
r_mcbond_other	0.344
r_symmetry_vdw_other	0.277
r_symmetry_hbond_refined	0.248
r_symmetry_vdw_refined	0.244
r_nbd_refined	0.209
r_nbd_other	0.193
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.11
r_nbtor_other	0.094
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_bond_other_d	0.003
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	1626
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	41

Software

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