3NY0 | pdb_00003ny0

Crystal Structure of UreE from Helicobacter pylori (Ni2+ bound form)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LA0	PDB entry 3LA0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	13% PEG 20000, 0.1M MES pH 5.5, vapor diffusion, sitting drop, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.057	α = 90
b = 91.057	β = 90
c = 202.823	γ = 90

Symmetry
Space Group	P 41 21 2

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 225 mm CCD		2010-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.4849	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.1	46.63	85.7	0.096	12.7	10.1		14069

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)
	3.1	3.21	38.9		0.293		5.7	617

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	PDB entry 3LA0	3.09	46.63	14043	695	85.96	0.2477	0.2453	0.2396	0.299	0.3008	RANDOM	93.598

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]
3.57			3.57		-7.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.292
r_dihedral_angle_3_deg	25.68
r_dihedral_angle_4_deg	20.867
r_dihedral_angle_1_deg	10.172
r_scangle_it	3.624
r_angle_refined_deg	2.057
r_scbond_it	1.953
r_mcangle_it	1.624
r_mcbond_it	0.849
r_chiral_restr	0.136
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4773
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing