4JG3 | pdb_00004jg3

Crystal structure of catabolite repression control protein (crc) from Pseudomonas aeruginosa

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JC5	PDB ENTRY 2jc5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295.15	10%(w/v) PEG1500, 40mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.659	α = 90
b = 74.659	β = 90
c = 123.161	γ = 120

Symmetry
Space Group	P 32 2 1

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 315r	mirrors	2012-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9000	ESRF	ID23-1

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	1.8	44.59	99.5	0.104	13.9	11	37275	37261			31.4

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	1.8	1.84	95.2		0.833	1.7	6.1	2073

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 2jc5	1.8	44.59	35360	1856	99.38	0.19529	0.19397	0.2	0.2199	0.22	RANDOM	42.784

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]
1.39	1.39		1.39		-4.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.783
r_dihedral_angle_4_deg	18.739
r_dihedral_angle_3_deg	15.093
r_dihedral_angle_1_deg	6.885
r_angle_refined_deg	2.009
r_angle_other_deg	1.001
r_chiral_restr	0.146
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2123
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling