7EFY | pdb_00007efy

Crystal structure of retroviral protease-like domain of Ddi1 from Cryptosporidium hominis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7D66

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6	291	0.1 M MES-sodium hydroxide (pH 6.0), 30% polyacrylate sodium salt and 10% ethanol

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.559	α = 90
b = 81.559	β = 90
c = 142.181	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	100	PIXEL	DECTRIS PILATUS 6M		2020-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	0.9918	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.8	63.26	100	0.99	11.1	7.5		4686

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.8	100		0.84	2.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7D66	2.8	47.439	4683	222	99.915	0.186	0.1836	0.19	0.2338	0.23	85.776

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]
3.332	1.666		3.332		-10.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.993
r_lrange_it	17.763
r_dihedral_angle_3_deg	16.27
r_scangle_it	15.591
r_scbond_it	11.637
r_mcangle_it	11.21
r_mcbond_it	7.912
r_dihedral_angle_1_deg	6.679
r_dihedral_angle_4_deg	2.96
r_angle_refined_deg	1.497

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.993
r_lrange_it	17.763
r_dihedral_angle_3_deg	16.27
r_scangle_it	15.591
r_scbond_it	11.637
r_mcangle_it	11.21
r_mcbond_it	7.912
r_dihedral_angle_1_deg	6.679
r_dihedral_angle_4_deg	2.96
r_angle_refined_deg	1.497
r_nbtor_refined	0.323
r_symmetry_nbd_refined	0.298
r_nbd_refined	0.237
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.111
r_chiral_restr	0.104
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	852
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.