6CKK

N. meningitidis CMP-sialic acid synthetase in the presence of CTP and Ca2+

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.1 M imidazole pH 8, 6% PEG 8000, and 0.2M calcium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.19	α = 90
b = 69.56	β = 90
c = 158.21	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	CCD	ADSC QUANTUM 315r		2015-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.03316	SSRL	BL7-1

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	1.8	79.11	93.8	0.048	0.998	16.64	3.35		42666

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	87.7		0.291	0.92	3.56	3.32

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	1EYR	1.8	79.11	40429	2171	93.74	0.20435	0.2019	0.24958	RANDOM	22.468

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]
0.26			0.54		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.957
r_dihedral_angle_3_deg	13.578
r_dihedral_angle_4_deg	12.357
r_long_range_B_refined	7.648
r_long_range_B_other	7.572
r_dihedral_angle_1_deg	6.285
r_scangle_other	4.001
r_mcangle_other	3.06
r_mcangle_it	3.057
r_scbond_it	2.564
r_scbond_other	2.563
r_mcbond_it	1.948
r_mcbond_other	1.928
r_angle_refined_deg	1.728
r_angle_other_deg	1.026
r_chiral_restr	0.105
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3441
Nucleic Acid Atoms
Solvent Atoms	680
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing