3LA0 | pdb_00003la0

Crystal Structure of UreE from Helicobacter pylori (metal of unknown identity bound)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3L9Z	UreE in apo form (PDB code 3L9Z)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5	295	16% PEG 8000, 5% glycerol, 0.1M Sodium Citrate pH 5.0, vapor diffusion, sitting drop, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.557	α = 90
b = 85.557	β = 90
c = 202.574	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	MAR165		2008-12-19		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID		APS	31-ID

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	2.86	45.06	99.4	0.12	8.7	23.3		18190

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)
	2.86	2.96	97.3		0.347		9.7

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	UreE in apo form (PDB code 3L9Z)	2.86	45.06	17182	926	99.31	0.27957	0.27817	0.28	0.30486	0.3	RANDOM	63.314

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]
2.09			2.09		-4.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.458
r_dihedral_angle_4_deg	22.68
r_dihedral_angle_3_deg	20.595
r_dihedral_angle_1_deg	8.08
r_scangle_it	5.211
r_scbond_it	2.959
r_mcangle_it	2.43
r_angle_refined_deg	1.844
r_mcbond_it	1.351
r_symmetry_vdw_refined	0.421
r_nbtor_refined	0.324
r_nbd_refined	0.263
r_symmetry_hbond_refined	0.22
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.118
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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	4413
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing