2IAY | pdb_00002iay

Crystal structure of a duf1831 family protein (lp2179) from lactobacillus plantarum at 1.20 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	10.5	277	0.2M NaCl, 20.0% PEG-8000, 0.1M CAPS, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 10.5
2	VAPOR DIFFUSION, SITTING DROP, NANODROP	9	277	20.0% PEG-6000, 0.1M Bicine, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 9.0

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.289	α = 90
b = 47.896	β = 90
c = 58.01	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	100	CCD	ADSC QUANTUM 315		2006-08-31
2	2	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2006-08-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9798	ALS	8.2.2
2	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.94926,0.97939,0.97925	APS	23-ID-D

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
2	1.198	28.928	90.4	0.069	0.069	6.1	6.2		29115

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)
2	1.2	1.23	50.7		0.204	0.204	3.7	1.4	1165

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	1.2	28.928	29080	1488	90.06	0.121	0.12	0.13	0.147	0.15	RANDOM	8.861

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]
0.85			-0.06		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.103
r_dihedral_angle_4_deg	15.509
r_dihedral_angle_3_deg	12.632
r_sphericity_free	8.569
r_dihedral_angle_1_deg	5.894
r_scangle_it	5.678
r_scbond_it	4.84
r_sphericity_bonded	4.255
r_mcangle_it	3.211
r_mcbond_it	2.727
r_rigid_bond_restr	2.275
r_angle_refined_deg	1.646
r_mcbond_other	1.519
r_angle_other_deg	0.997
r_symmetry_vdw_other	0.293
r_nbd_refined	0.217
r_nbd_other	0.199
r_symmetry_vdw_refined	0.189
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.129
r_chiral_restr	0.097
r_nbtor_other	0.09
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	885
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	6

Software

Software
Software Name	Purpose
MolProbity	model building
SOLVE	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling