2Q4U

Ensemble refinement of the crystal structure of an EF-hand protein from Danio rerio Dr.36843

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BE4	PDB entry 2BE4

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.884	α = 90
b = 52.748	β = 90
c = 114.364	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray						M	SINGLE WAVELENGTH

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	Re-refinement using ensemble model	THROUGHOUT	PDB entry 2BE4	2.1	44.17	17332	885	98.7	0.154	0.154	0.242	RANDOM	33.5

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]
4.53			-4		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.6
c_scangle_it	2.81
c_mcangle_it	2.26
c_scbond_it	2.08
c_mcbond_it	1.52
c_angle_deg	1.4
c_improper_angle_d	0.93
c_bond_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2203
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CNS	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 R01GM157729.