2JCG | pdb_00002jcg

Apo form of the catabolite control protein A (ccpA) from bacillus megaterium, with the DNA binding domain

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		3% PEG 3000, 100 MM CACL2, 10% (V/V) GLYCEROL, 100 MM TRIS-HCL PH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.6	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.45	α = 90
b = 74.45	β = 90
c = 238.84	γ = 120

Symmetry
Space Group	P 61 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	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11

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	2.6	30	98.6	0.05	24.8	6.5		14161		-3

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	2.6	2.7			0.44	3.7

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	PDB ENTRY 1SXG	2.6	19.6	11615	1036	98.7	0.234	0.229	0.22	0.297	0.28	RANDOM	46.14

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]
0.09	0.05		0.09		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.023
r_dihedral_angle_4_deg	20.22
r_dihedral_angle_3_deg	17.519
r_dihedral_angle_1_deg	5.984
r_scangle_it	4.118
r_scbond_it	2.568
r_angle_refined_deg	1.3
r_mcangle_it	0.862
r_mcbond_it	0.437
r_nbtor_refined	0.308
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.197
r_symmetry_hbond_refined	0.165
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.091
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2427
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing