5TR7

Crystal structure of a putative D-alanyl-D-alanine carboxypeptidase from Vibrio cholerae O1 biovar eltor str. N16961

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NZO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	0.2 M Sodium Nitrate, 0.1 M Bis-Tris propane, 20% PEG3350

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.749	α = 90
b = 88.749	β = 90
c = 85.425	γ = 120

Symmetry
Space Group	P 31

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	3.0 Undulator	2016-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	30	100	0.066	0.97	36.6	5.8		47191

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		0.75	3.1	5.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	1NZO	2.05	30	44920	2246	99.94	0.19321	0.19086	0.23774	RANDOM	65.043

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]
2.77	1.38		2.77		-8.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.259
r_dihedral_angle_4_deg	18.573
r_dihedral_angle_3_deg	12.942
r_long_range_B_refined	8.086
r_long_range_B_other	8.086
r_scangle_other	6.44
r_mcangle_it	4.927
r_mcangle_other	4.927
r_scbond_it	4.789
r_scbond_other	4.784
r_mcbond_it	3.844
r_mcbond_other	3.841
r_dihedral_angle_1_deg	3.324
r_angle_refined_deg	2.028
r_angle_other_deg	0.993
r_chiral_restr	0.132
r_gen_planes_refined	0.027
r_gen_planes_other	0.021
r_bond_refined_d	0.018
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5772
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing