3OXK

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OMF	3OMF, with ligand and water molecules removed

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 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 R01GM133198.