2I8D | pdb_00002i8d

Crystal structure of an uncharacterized conserved protein of COG5646 (ZP_00384875.1) from Lactobacillus casei ATCC 334 at 1.69 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	4	277	1.0M LiCl, 20.0% PEG-6000, 0.1M Citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, <NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP, NANODROP

Crystal Properties
Matthews coefficient	Solvent content
2.557158	51.899723

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.946	α = 90
b = 69.276	β = 90
c = 90.872	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	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	APS BEAMLINE 23-ID-D	0.94926,0.97925	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
1	1.6	29.775	99.9	0.081	0.081	4.7	3.6		34612			23.99

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	1.69	1.73	100		0.662	0.662	1.1	3.7	2504

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	1.69	29.775	34565	1740	99.84	0.169	0.168	0.17	0.197	0.2	RANDOM	21.732

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]
0.86			0.13		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.161
r_dihedral_angle_4_deg	17.39
r_dihedral_angle_3_deg	13.892
r_scangle_it	5.27
r_dihedral_angle_1_deg	5.251
r_scbond_it	3.853
r_mcangle_it	2.579
r_mcbond_it	2.074
r_angle_refined_deg	1.365
r_angle_other_deg	0.866
r_mcbond_other	0.517
r_nbd_refined	0.24
r_symmetry_vdw_other	0.209
r_symmetry_vdw_refined	0.197
r_nbd_other	0.188
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.164
r_symmetry_hbond_refined	0.132
r_nbtor_other	0.085
r_chiral_restr	0.082
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1998
Nucleic Acid Atoms
Solvent Atoms	307
Heterogen Atoms	31

Software

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