Experiment: 3QJK

Structure of Calcium Binding Protein-1 from Entamoeba histolytica in complex with Lead

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	3.6	289	60-65% MPD, 50mM NaOAc, 5mM Pb(NO3)2, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.264	α = 90
b = 95.264	β = 90
c = 64.597	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	2008-06-05	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	3	30	87	0.054	0.0364	8.8	2.9	6777	6763

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.11	99.7		0.054	0.364	1.1	2.9

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2NXQ	3.001	28.082	1.39	6777	6763	685	99.72	0.2549	0.2518	0.2559	0.283	0.288	75.1336

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]
-8.9307			-8.9307		17.8614

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.722
f_angle_d	1.854
f_chiral_restr	0.101
f_bond_d	0.015
f_plane_restr	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	996
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	12

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
CNS	refinement
AUTOMAR	data reduction
PHENIX	refinement