2O20 | pdb_00002o20

Crystal structure of transcription regulator CcpA of Lactococcus lactis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8	296	PEG 3350 (22.5% (w/v), 100 mM Li2SO4, 100 mM Tris/HCl, VAPOR DIFFUSION, HANGING DROP, temperature 296K, pH 8.00

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.756	α = 90
b = 74.267	β = 102.36
c = 160.302	γ = 90

Symmetry
Space Group	P 1 21 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 4		2005-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	19.9	99.4	11.74	5.5		211799

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95	99.1		4.49	4.4

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 1ZVV	1.9	19.9	211799	201126	10565	99.4	0.177	0.176	0.18	0.211	0.22	RANDOM	29.7

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]
0.83		0.41	0.18		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.66
r_dihedral_angle_4_deg	19.107
r_dihedral_angle_3_deg	13.91
r_dihedral_angle_1_deg	5.84
r_scangle_it	3.14
r_scbond_it	1.984
r_angle_refined_deg	1.289
r_mcangle_it	1.253
r_angle_other_deg	0.808
r_mcbond_it	0.808
r_symmetry_vdw_refined	0.207
r_symmetry_vdw_other	0.2
r_nbd_refined	0.197
r_mcbond_other	0.194
r_nbd_other	0.167
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.15
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_other	0.114
r_nbtor_other	0.079
r_chiral_restr	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16891
Nucleic Acid Atoms
Solvent Atoms	1335
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing