3ULG | pdb_00003ulg

Crystal structure of Calcium-Binding Protein-1 from Entamoeba histolytica in complex with barium

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NXQ	PDB ENTRY 2NXQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.8	289	60-65% MPD, 0.05M Sodium acetate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.21	α = 90
b = 95.21	β = 90
c = 62.986	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2009-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.2	50	99.6	15.4	5.2		5485	1	2	103.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.31	99.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB ENTRY 2NXQ	3.2	50	1.8	5507	5485	234	96.63	0.25041	0.24707	0.25	0.31425	0.31	RANDOM	122.089

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]
-6.59	-3.29		-6.59		9.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.458
r_dihedral_angle_3_deg	19.544
r_dihedral_angle_1_deg	4.865
r_dihedral_angle_4_deg	3.458
r_angle_refined_deg	1.303
r_chiral_restr	0.079
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	966
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	6

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.