5UEJ

1.30 A crystal structure of DapE enzyme from Neisseria meningitidis MC58

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.2 M Lithium Sulfate, 0.1 M Tris:HCl pH 8.5, 1.26 M Ammonium Sulfate, 0.05 M DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.767	α = 90
b = 88.644	β = 90
c = 133.402	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS3 S 6M	Double Crystal	2016-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9795	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	1.3	40	99.4	0.08	22	7.4		217263

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32

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		THROUGHOUT	1.3	40	176526	9439	95.2	0.11497	0.113	0.15254	RANDOM	18.628

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]
0.12			-0.17		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	39.399
r_dihedral_angle_2_deg	35.703
r_dihedral_angle_4_deg	17.956
r_sphericity_bonded	16.081
r_dihedral_angle_3_deg	12.639
r_scangle_other	6.626
r_long_range_B_refined	6.391
r_dihedral_angle_1_deg	6.122
r_scbond_other	6.071
r_scbond_it	6.068
r_rigid_bond_restr	5.749
r_long_range_B_other	5.566
r_mcbond_other	2.867
r_mcbond_it	2.866
r_mcangle_it	2.863
r_mcangle_other	2.863
r_angle_refined_deg	2.435
r_angle_other_deg	1.322
r_chiral_restr	0.179
r_bond_refined_d	0.029
r_gen_planes_refined	0.014
r_gen_planes_other	0.004
r_bond_other_d	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5736
Nucleic Acid Atoms
Solvent Atoms	1129
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing