3FIU | pdb_00003fiu

Structure of NMN synthetase from Francisella tularensis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KQP	PDB ENTRY 1kqp

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M K/Na tartrate, 16% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.432	α = 90
b = 126.438	β = 90
c = 152.531	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++	Osmic VariMax		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.85	50	94	0.044				79468

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1kqp	1.85	40	75114	3935	93.86	0.18662	0.18411	0.18	0.23338	0.23	RANDOM	26.216

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]
0.35			0.18		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.516
r_dihedral_angle_4_deg	19.147
r_dihedral_angle_3_deg	14.863
r_scangle_it	5.884
r_dihedral_angle_1_deg	5.61
r_scbond_it	3.78
r_mcangle_it	2.316
r_angle_refined_deg	1.391
r_mcbond_it	1.384
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.262
r_symmetry_hbond_refined	0.217
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.096
r_metal_ion_refined	0.043
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7564
Nucleic Acid Atoms
Solvent Atoms	812
Heterogen Atoms	140

Software

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