3K69 | pdb_00003k69

CRYSTAL STRUCTURE OF A PUTATIVE TRANSCRIPTIONAL REGULATOR (LP_0360) FROM LACTOBACILLUS PLANTARUM AT 1.95 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	0.2000M Na2HPO4, 20.0000% PEG-3350, No Buffer pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.173	α = 90
b = 38.054	β = 110.73
c = 42.275	γ = 90

Symmetry
Space Group	C 1 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-07-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97959,0.97886	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.95	28.307	97.8	0.093	0.093	10.9	3.6		12340			22.604

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	80.2		0.691	0.691	1	2.8	729

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.95	28.307	12306	599	97.45	0.174	0.172	0.18	0.218	0.22	RANDOM	25.623

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]
-1.43		-0.93	0.84		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.856
r_dihedral_angle_4_deg	12.786
r_dihedral_angle_3_deg	11.868
r_dihedral_angle_1_deg	6.439
r_scangle_it	6.078
r_scbond_it	5.012
r_mcangle_it	3.223
r_mcbond_it	2.27
r_angle_refined_deg	1.393
r_angle_other_deg	0.998
r_mcbond_other	0.534
r_symmetry_vdw_other	0.286
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.21
r_symmetry_hbond_refined	0.191
r_nbtor_refined	0.178
r_nbd_other	0.177
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.089
r_nbtor_other	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1170
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction