6LTW | pdb_00006ltw

Crystal structure of Apo form of I122A/I330A variant of S-adenosylmethionine synthetase from Cryptosporidium hominis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ODJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	285.15	12 % MPD (v/v), 12 % PEG 1000 (w/v) , 12 % PEG 3350 (w/v), 0.1 MES/imidazole pH 6.5, 0.03 M sodium phosphate dibasic dihydrate, 0.03 M ammonium sulfate and 0.03 M sodium nitrate.

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.877	α = 90
b = 100.36	β = 95.86
c = 66.842	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	PIXEL	DECTRIS PILATUS3 6M		2019-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9802	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.65	48.08	99	0.068	0.999	14.5	6.7		97449

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	85.3		0.972	0.765		5.7

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	4ODJ	1.65	48.08	92649	4768	99.08	0.158	0.1562	0.17	0.191	0.2	RANDOM	29.104

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]
0.53		-0.13	-1.33		0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.594
r_dihedral_angle_4_deg	17.221
r_dihedral_angle_3_deg	14.253
r_dihedral_angle_1_deg	6.512
r_angle_refined_deg	2.292
r_angle_other_deg	1.009
r_chiral_restr	0.146
r_bond_refined_d	0.025
r_gen_planes_refined	0.012
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.594
r_dihedral_angle_4_deg	17.221
r_dihedral_angle_3_deg	14.253
r_dihedral_angle_1_deg	6.512
r_angle_refined_deg	2.292
r_angle_other_deg	1.009
r_chiral_restr	0.146
r_bond_refined_d	0.025
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5886
Nucleic Acid Atoms
Solvent Atoms	580
Heterogen Atoms	24

Software

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

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.