3LP5 | pdb_00003lp5

The crystal structure of the putative cell surface hydrolase from Lactobacillus plantarum WCFS1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	1.6M tri-sodium citrate dehydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.68	α = 90
b = 122.154	β = 90
c = 38.659	γ = 90

Symmetry
Space Group	P 21 21 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	ADSC QUANTUM 315r	mirrors	2008-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-ID

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	61.08	99.4	0.187	15.36	8.1	16365	16267	2	1.3

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	2.052	96.7		0.665	1.3	3.9	1243

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2	61.08	16365	16267	866	99.4	0.17768	0.17462	0.18	0.23647	0.24	RANDOM	19.065

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]
-1.38			0.05		1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.229
r_dihedral_angle_4_deg	15.983
r_dihedral_angle_3_deg	15.692
r_dihedral_angle_1_deg	6.238
r_scangle_it	5.649
r_scbond_it	3.328
r_mcangle_it	1.97
r_angle_refined_deg	1.728
r_mcbond_it	1.081
r_chiral_restr	0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.229
r_dihedral_angle_4_deg	15.983
r_dihedral_angle_3_deg	15.692
r_dihedral_angle_1_deg	6.238
r_scangle_it	5.649
r_scbond_it	3.328
r_mcangle_it	1.97
r_angle_refined_deg	1.728
r_mcbond_it	1.081
r_chiral_restr	0.13
r_bond_refined_d	0.022
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1980
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.