3SJS

Crystal structure of URE3-binding protein from Entamoeba histolytica, (D127A,N129A) mutant, native form

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	290	Internal tracking number 215760A3. Focus screen based on CryoFull G6. 1 uL 40% PEG600, 0.1 M citrate pH 4.56 + 1 uL EnhiA.01648.a.D18 PD00123 (VCID3088) at 9.5 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.25	α = 90
b = 68.29	β = 90
c = 130.89	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+		2010-06-16	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	1.9	38.29	99.4	0.055	17.42	5.05		16665		-3	30.04

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	1.9	1.95	96.3		0.431	2.4	2.746

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3SIA	1.9	38.29	16655	651	99.86	0.174	0.172	0.221	RANDOM	23.09

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]
			0.9		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.761
r_dihedral_angle_4_deg	18.892
r_dihedral_angle_3_deg	13.457
r_dihedral_angle_1_deg	5.409
r_scangle_it	3.803
r_scbond_it	2.417
r_angle_refined_deg	1.452
r_mcangle_it	1.338
r_angle_other_deg	0.954
r_mcbond_it	0.719

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.761
r_dihedral_angle_4_deg	18.892
r_dihedral_angle_3_deg	13.457
r_dihedral_angle_1_deg	5.409
r_scangle_it	3.803
r_scbond_it	2.417
r_angle_refined_deg	1.452
r_mcangle_it	1.338
r_angle_other_deg	0.954
r_mcbond_it	0.719
r_mcbond_other	0.189
r_chiral_restr	0.085
r_bond_refined_d	0.016
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	1722
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	2

Software

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

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.