2ODM | pdb_00002odm

Crystal structure of S. aureus YlaN, an essential leucine rich protein involved in the control of cell shape

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	0.2M Sodium acetate, 0.1M Tris-HCl pH 8.5, 20% PEG4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.425	α = 90
b = 42.771	β = 92.42
c = 62.593	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	MAR CCD 165 mm		2005-06-26	M	MAD
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	0.98000	SRS	PX10.1
2	SYNCHROTRON	SRS BEAMLINE PX9.6	1.50000	SRS	PX9.6

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	2.24	25	100	0.079	0.079	10.5	3.6	7464				51

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	2.24		99.7		0.429	0.429	2.6	3.6	1072

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	MAD	THROUGHOUT	2.24	15	7464	7464	365	99.16	0.22659	0.22373	0.22	0.28317	0.28	RANDOM	59.86

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]
-2.13		-0.05	-2.32		4.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.665
r_dihedral_angle_4_deg	25.064
r_dihedral_angle_3_deg	18.898
r_scangle_it	10.97
r_scbond_it	8.945
r_mcangle_it	8.774
r_mcbond_it	7.141
r_dihedral_angle_1_deg	4.11
r_angle_refined_deg	1.031
r_nbtor_refined	0.278

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.665
r_dihedral_angle_4_deg	25.064
r_dihedral_angle_3_deg	18.898
r_scangle_it	10.97
r_scbond_it	8.945
r_mcangle_it	8.774
r_mcbond_it	7.141
r_dihedral_angle_1_deg	4.11
r_angle_refined_deg	1.031
r_nbtor_refined	0.278
r_nbd_refined	0.186
r_symmetry_vdw_refined	0.16
r_symmetry_hbond_refined	0.101
r_xyhbond_nbd_refined	0.067
r_chiral_restr	0.054
r_bond_refined_d	0.007
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1297
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SOLVE	phasing
SHARP	phasing

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.