5YQ8

Crystal structure of retroviral protease-like domain of Ddi1 from Leishmania major

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	4.5	293	0.1 M sodium acetate trihydrate, 30 % polyethylene glycol 1500

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.53	α = 90
b = 80.39	β = 90
c = 85.45	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2016-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.25	58.55	96.76	0.136	0.136	0.971	5.9	2.6		22170

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.32	98.7		0.34	0.339	0.324	2.7	2.4

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	2I1A	2.25	42.72	21101	1069	96.76	0.16788	0.1642	0.23981	RANDOM	16.669

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]
1.33		2.12	-3.1		1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.146
r_dihedral_angle_3_deg	15.55
r_dihedral_angle_4_deg	14.199
r_dihedral_angle_1_deg	6.873
r_long_range_B_refined	4.967
r_long_range_B_other	4.771
r_mcangle_it	2.341
r_mcangle_other	2.34
r_scangle_other	1.883
r_angle_refined_deg	1.855
r_mcbond_it	1.486
r_mcbond_other	1.479
r_scbond_it	1.215
r_scbond_other	1.215
r_angle_other_deg	1.095
r_chiral_restr	0.098
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3927
Nucleic Acid Atoms
Solvent Atoms	480
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing