5Z01

Native Escherichia coli L,D-carboxypeptidase A (LdcA)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.02M Tris pH 8.5, 0.2M sodium thiocyanate, 12% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.949	α = 90
b = 89.069	β = 90
c = 93.772	γ = 90

Symmetry
Space Group	I 2 2 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	PIXEL	DECTRIS PILATUS 300K		2016-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

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	1.75	46.9	99.9	0.073	0.999	19.4	9		33235

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.77	99.9		1.016	0.37	0.889	2.2	9.3

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.75	46.886	33251	1631	99.946	0.179	0.179	0.1762	0.2246	RANDOM	29.459

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]
4.444			-1.687		-2.756

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.029
r_dihedral_angle_4_deg	23.032
r_dihedral_angle_3_deg	13.916
r_lrange_it	7.244
r_lrange_other	7.175
r_dihedral_angle_1_deg	6.322
r_scangle_it	5.714
r_scangle_other	5.711
r_scbond_it	3.785
r_scbond_other	3.783
r_mcangle_other	3.565
r_mcangle_it	3.564
r_mcbond_it	2.672
r_mcbond_other	2.671
r_angle_refined_deg	1.803
r_angle_other_deg	1.047
r_nbd_other	0.275
r_nbd_refined	0.206
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.17
r_symmetry_nbd_refined	0.169
r_symmetry_nbd_other	0.167
r_symmetry_xyhbond_nbd_refined	0.161
r_chiral_restr	0.112
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2371
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing