3UFK | pdb_00003ufk

Crystal structure of UndA complexed with Iron Nitrilotriacetate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	100 mM MES, 50 mM NaCl, 50 mM MgCl2, 15% PEG5000, 20% Glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.5	α = 90
b = 105.87	β = 90
c = 151.52	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	100	CCD	MARMOSAIC 300 mm CCD		2011-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.917	Diamond	I04-1

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	2.1	69.5	99.5	0.078	0.078	9.1	4.4		65620		1.9

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	2.1	2.15	99.3		0.378	0.378	4.6	4.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.1	61.61	62231	62230	3323	100	0.1579	0.1554	0.16	0.20463	0.2	RANDOM	25.578

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]
-0.04			-0.01		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.53
r_dihedral_angle_3_deg	15.233
r_dihedral_angle_4_deg	14.199
r_dihedral_angle_1_deg	7.559
r_scangle_it	5.684
r_scbond_it	4.171
r_mcangle_it	2.569
r_mcbond_it	1.685
r_angle_refined_deg	1.463
r_chiral_restr	0.114
r_gen_planes_refined	0.018
r_bond_refined_d	0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5948
Nucleic Acid Atoms
Solvent Atoms	996
Heterogen Atoms	558

Software

Software
Software Name	Purpose
xia2	data scaling
PHASER	phasing
REFMAC	refinement
xia2	data reduction