5UTU | pdb_00005utu

2.65 Angstrom Resolution Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with SAH and NAD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5HM8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	Protein: 9.3 mg/ml, 0.5M Sodium chloride, 0.1M Tris HCl (pH 8.3), 1mM Adenosine, 1mM NAD, 1mM Homocysteine; Screen: Classics II (F6), 0.2M Ammonium sulfate, 0.1M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.906	α = 90
b = 185.834	β = 97.98
c = 121.619	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	CCD	MARMOSAIC 225 mm CCD	C(111)	2016-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rpim I (All)	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	2.65	30	100	0.099	0.099	0.047	16.2	5.2		137384		-3	58.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.7	100		0.646	0.646	0.307	0.843	2.8	5.2

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	5HM8	2.65	30	130306	6930	99.91	0.172	0.17041	0.17	0.20208	0.2	RANDOM	52.2

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]
0.74		-0.55	-2.47		1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.326
r_dihedral_angle_4_deg	13.195
r_dihedral_angle_3_deg	11.373
r_long_range_B_refined	5.86
r_long_range_B_other	5.847
r_scangle_other	3.796
r_mcangle_it	3.187
r_mcangle_other	3.187
r_dihedral_angle_1_deg	2.643
r_scbond_it	2.392
r_scbond_other	2.39
r_mcbond_it	1.922
r_mcbond_other	1.921
r_angle_refined_deg	1.586
r_angle_other_deg	0.91
r_chiral_restr	0.089
r_gen_planes_refined	0.023
r_gen_planes_other	0.02
r_bond_refined_d	0.009
r_bond_other_d	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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31128
Nucleic Acid Atoms
Solvent Atoms	931
Heterogen Atoms	837

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing