5BMQ

Crystal structure of L,D-transpeptidase (Yku) from Stackebrandtia nassauensis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		297	1.6 M ammonium sulfate, 0.1 M MES, pH 6.5, 10% dioxane

Crystal Properties
Matthews coefficient	Solvent content
4.56	73.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.356	α = 90
b = 143.356	β = 90
c = 143.356	γ = 90

Symmetry
Space Group	I 21 3

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		2013-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97899	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	2.05	50	99.7	0.077	12.7	7.3		30882

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	2.05	2.09	100		0.86		7.3	1547

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.05	32.08	28664	1521	97.51	0.1549	0.1536	0.1781	RANDOM	29.718

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.503
r_dihedral_angle_2_deg	31.424
r_dihedral_angle_3_deg	11.497
r_dihedral_angle_4_deg	11.483
r_sphericity_bonded	8.999
r_dihedral_angle_1_deg	4.953
r_rigid_bond_restr	1.311
r_angle_refined_deg	0.949
r_angle_other_deg	0.657
r_chiral_restr	0.057

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	37.503
r_dihedral_angle_2_deg	31.424
r_dihedral_angle_3_deg	11.497
r_dihedral_angle_4_deg	11.483
r_sphericity_bonded	8.999
r_dihedral_angle_1_deg	4.953
r_rigid_bond_restr	1.311
r_angle_refined_deg	0.949
r_angle_other_deg	0.657
r_chiral_restr	0.057
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1607
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	22

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.