3BD1 | pdb_00003bd1

Structure of the Cro protein from putative prophage element Xfaso 1 in Xylella fastidiosa strain Ann-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HIN	PDB entry 2HIN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	16% glycerol, 1.5 M ammonium sulfate, 0.1 M Tris, 1 mM TCEP-hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.97	α = 90
b = 66.97	β = 90
c = 54.36	γ = 120

Symmetry
Space Group	P 32

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	ADSC QUANTUM 315		2005-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9002	APS	14-BM-C

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	1.4	58.03	98.6	0.048	13.3	3.61		53726			23.5

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)
1	1.4	1.45	99.7		0.386	3.2	3.65	5367

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	ACORN (DDM)	THROUGHOUT	PDB entry 2HIN	1.4	17.06	55642	52945	2697	98.5	0.147	0.147	0.16	0.182	0.19	RANDOM	18.77

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]
-0.73	-0.37		-0.73		1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.92
r_sphericity_free	18.588
r_dihedral_angle_4_deg	15.105
r_dihedral_angle_3_deg	12.905
r_scangle_it	12.145
r_sphericity_bonded	9.454
r_scbond_it	9.176
r_mcangle_it	5.579
r_rigid_bond_restr	5.312
r_mcbond_it	5.283
r_dihedral_angle_1_deg	4.354
r_mcbond_other	3.971
r_angle_other_deg	2.7
r_angle_refined_deg	1.792
r_symmetry_vdw_other	0.333
r_symmetry_vdw_refined	0.243
r_nbd_other	0.237
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.177
r_symmetry_hbond_refined	0.147
r_chiral_restr	0.103
r_nbtor_other	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1441
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	35

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDISPLAYF	data collection
d*TREK	data reduction
ACORN	phasing