3OXK

Crystal structure of a histidine triad family protein from Entamoeba histolytica, bound to GMP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	290	Internal tracking number 217759B6. JCSG screen condition B6: 40% v/v ethanol, 5% w/v PEG 1000, phosphate-citrate buffer pH 4.2, EnhiA.01296.a.A1 PS00632 at 83.2 mg/ml + ~30 mM GMP, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.66	α = 90
b = 60.86	β = 90
c = 67.93	γ = 90

Symmetry
Space Group	C 2 2 21

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	RIGAKU SATURN 944		2010-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.541780

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	1.55	27.77	90.3	0.05	25.18	6.6	16495	14890		-3	18.008

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	1.55	1.59	82.4		0.391	3.8	5.2	1185

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	3OMF, with ligand and water molecules removed	1.55	27.77	16495	14847	712	90.01	0.159	0.159	0.157	0.208	RANDOM	11.794

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]
0.03			-0.61		0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.591
r_dihedral_angle_4_deg	19.829
r_dihedral_angle_3_deg	11.262
r_dihedral_angle_1_deg	6.264
r_scangle_it	3.162
r_scbond_it	2.049
r_angle_refined_deg	1.628
r_mcangle_it	1.29
r_angle_other_deg	0.898
r_mcbond_it	0.756

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.591
r_dihedral_angle_4_deg	19.829
r_dihedral_angle_3_deg	11.262
r_dihedral_angle_1_deg	6.264
r_scangle_it	3.162
r_scbond_it	2.049
r_angle_refined_deg	1.628
r_mcangle_it	1.29
r_angle_other_deg	0.898
r_mcbond_it	0.756
r_mcbond_other	0.216
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	897
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	28

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
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.