2WDT

Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XD3	PDB ENTRY 1XD3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		100 MM BIS-TRIS PH 5.5, 200 MM NACL, 25 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.3	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.4	α = 90
b = 75.3	β = 90
c = 85.7	γ = 90

Symmetry
Space Group	P 21 21 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 CCD	TRIPLE STRIPED VERTICAL AND HORIZANTAL FOCUSSING MIRRORS IN KIRKPATRICK- BAEZ GEOMETRY	2007-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C		APS	24-ID-C

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	2.3	30	98.1	0.11	8	5.7		39592		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	2.3	2.36	90.2		0.45	2.1	3.3

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 1XD3	2.3	19.85	38252	1062	100	0.188	0.187	0.2	0.235	0.24	RANDOM	35.33

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]
-0.8			3.3		-2.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.591
r_dihedral_angle_4_deg	22.751
r_dihedral_angle_3_deg	17.4
r_dihedral_angle_1_deg	5.939
r_scangle_it	3.121
r_scbond_it	1.932
r_mcangle_it	1.354
r_angle_refined_deg	1.319
r_angle_other_deg	0.908
r_mcbond_it	0.71
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4564
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing