4TNN | pdb_00004tnn

Crystal structure of Escherichia coli protein YodA in complex with Ni - artifact of purification.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OEJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.3 ul of 9.6 mg/ml protein in 50mM Tris pH 7.9, 300 mM NaCl and 0.5mM TCEP were mixed with 0.3 ul of the SaltRx condition #65 (2.5 M Ammonium sulfate, 0.1 M BIS-TRIS propane pH 7.0) and equilibrated against 1.5 M NaCl in MRC 2 drops 96 Well Crystallization Plate (Swissci)

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.583	α = 90
b = 76.583	β = 90
c = 61.944	γ = 120

Symmetry
Space Group	P 31 2 1

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	MARMOSAIC 300 mm CCD		2013-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.978	APS	21-ID-G

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	1.95	50	99.9	0.08	0.08	9	7.3	15647	15635		-3	28.4

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	1.95	1.98	100		0.767	2.41	7.4	750

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1OEJ	1.951	50	15616	782	99.94	0.1689	0.1666	0.17	0.2154	0.21	RANDOM	36.632

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]
0.2	0.1		0.2		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.206
r_dihedral_angle_4_deg	15.162
r_dihedral_angle_3_deg	14.378
r_dihedral_angle_1_deg	6.492
r_mcangle_it	2.02
r_angle_refined_deg	1.5
r_mcbond_other	1.417
r_mcbond_it	1.416
r_angle_other_deg	0.772
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.206
r_dihedral_angle_4_deg	15.162
r_dihedral_angle_3_deg	14.378
r_dihedral_angle_1_deg	6.492
r_mcangle_it	2.02
r_angle_refined_deg	1.5
r_mcbond_other	1.417
r_mcbond_it	1.416
r_angle_other_deg	0.772
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1546
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	31

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXDE	phasing
MLPHARE	phasing
DM	phasing
Coot	model building
PDB_EXTRACT	data extraction
REFMAC	refinement
DENZO	data reduction
SCALEPACK	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.