3L9Z | pdb_00003l9z

Crystal Structure of UreE from Helicobacter pylori (apo form)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	295	17% PEG 8000, 0.1M Sodium Citrate pH 5.0, vapor diffusion, sitting drop, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.011	α = 90
b = 131.011	β = 90
c = 51.267	γ = 120

Symmetry
Space Group	P 64 2 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	MAR CCD 165 mm		2008-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	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	2.08	42.88	99.8	0.05	18.7	15.7		16040

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)
	2.08	2.15	99.5		0.496		8.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.08	42.88	15182	802	99.48	0.22277	0.2211	0.22	0.25488	0.26	RANDOM	41.904

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]
1.65	0.82		1.65		-2.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.74
r_dihedral_angle_3_deg	16.566
r_dihedral_angle_4_deg	15.089
r_dihedral_angle_1_deg	6.889
r_scangle_it	2.979
r_scbond_it	1.769
r_angle_refined_deg	1.309
r_mcangle_it	1.26
r_mcbond_it	0.746
r_nbtor_refined	0.301
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.216
r_symmetry_vdw_refined	0.179
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
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	1170
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms

Software

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