4ODJ

Crystal structure of a putative S-adenosylmethionine synthetase from Cryptosporidium hominis in complex with S-adenosyl-methionine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	290	Microlytics MCSG1 screen, g11: 100mM Na2HPO4/citric acid pH 4.2, 40% PEG 300; CrhoA.00729.a.B1.PW37315 at 28.4mg/ml + 2.5mM S-Adenosyl-Methionine; tray 247830, puck QJI2-2, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.86	α = 90
b = 117.86	β = 90
c = 54.04	γ = 120

Symmetry
Space Group	P 32 2 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	RAYONIX MX-225		2013-10-16	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)	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	1.6	50	99.5	0.058	14.33	3.7	57078	56815		-3	24.262

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	1.6	1.64	99.5		0.56	2.39

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3SO4 modified with CCP4 program chainsaw	1.6	50	57078	56815	2803	99.53	0.1456	0.1445	0.1652	RANDOM	20.8199

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]
0.11	0.05		0.11		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.576
r_dihedral_angle_4_deg	16.476
r_dihedral_angle_3_deg	12.14
r_dihedral_angle_1_deg	6.013
r_angle_refined_deg	1.645
r_mcangle_it	1.392
r_mcbond_it	0.845
r_mcbond_other	0.845
r_angle_other_deg	0.824
r_chiral_restr	0.104

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.576
r_dihedral_angle_4_deg	16.476
r_dihedral_angle_3_deg	12.14
r_dihedral_angle_1_deg	6.013
r_angle_refined_deg	1.645
r_mcangle_it	1.392
r_mcbond_it	0.845
r_mcbond_other	0.845
r_angle_other_deg	0.824
r_chiral_restr	0.104
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2934
Nucleic Acid Atoms
Solvent Atoms	297
Heterogen Atoms	42

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.