6JTL

Crystal structure of NagZ from Neisseria gonorrhoeae in complex with zinc ion

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6JTI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.2 M Sodium acetate trihydrate, 20% w/v polyethylene glycol 3,350 pH8.0

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.805	α = 90
b = 90.992	β = 90
c = 103.325	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	IMAGE PLATE	RIGAKU RAXIS IV++		2018-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.4	50	99.7	0.121	23.4	6.1		25780

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	2.4	2.44	98.3		0.56	2.5	5.6

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	6JTI	2.4	50	24423	1306	99.32	0.2053	0.20298	0.24919	RANDOM	43.887

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]
-2.37			3.6		-1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.622
r_dihedral_angle_4_deg	18.722
r_dihedral_angle_3_deg	14.802
r_long_range_B_refined	6.878
r_long_range_B_other	6.868
r_dihedral_angle_1_deg	6.182
r_scangle_other	4.352
r_mcangle_it	3.718
r_mcangle_other	3.718
r_scbond_it	2.595
r_scbond_other	2.595
r_mcbond_it	2.32
r_mcbond_other	2.319
r_angle_refined_deg	1.339
r_angle_other_deg	0.931
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	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	5131
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	4

Software

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