1ZB8 | pdb_00001zb8

Crystal structure of Xylella fastidiosa organic peroxide resistance protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N2F	PDB ENTRY 1N2F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.7	293	Peg 4000, Tris-HCl, 0,29mM t-BOOH, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.19	55.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.697	α = 90
b = 91.697	β = 90
c = 157.178	γ = 120

Symmetry
Space Group	P 65 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	110	CCD	MARRESEARCH	mirrors	2004-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.453	LNLS	D03B-MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	79.31		0.061	10.3	7.4		15924

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53			0.267	2.8	7.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 1N2F	2.4	79.31	15858	15130	794	99.9	0.19491	0.19232	0.19	0.24371	0.24	RANDOM	27.664

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]
-0.74	-0.37		-0.74		1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.148
r_dihedral_angle_4_deg	15.972
r_dihedral_angle_3_deg	15.63
r_dihedral_angle_1_deg	6.121
r_scangle_it	3.228
r_scbond_it	1.993
r_angle_refined_deg	1.739
r_mcangle_it	1.395
r_mcbond_it	0.777
r_nbtor_refined	0.311
r_nbd_refined	0.247
r_symmetry_hbond_refined	0.161
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.148
r_symmetry_vdw_refined	0.123
r_bond_refined_d	0.012
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	2052
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
CCP4	data scaling
AMoRE	phasing