2D1Q

Crystal structure of the thermostable Japanese Firefly Luciferase complexed with MgATP

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	293	PEG4000, Lithium chrolide, ATP, magnesium chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.78	α = 90
b = 181.975	β = 90
c = 53.566	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	293	IMAGE PLATE	RIGAKU RAXIS IIC		1999-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	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	2.3	60	97.9	0.058	10.7	3.1	25394	25394	1	1

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)
	2.3	2.38	91.1		0.15	4	2.55	2304

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 1LCI	2.3	60	25353	24062	1291		0.18151	0.18151	0.17898	0.22766	RANDOM	22.972

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]
-1.64			-0.18		1.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.703
r_scangle_it	2.932
r_scbond_it	1.714
r_angle_refined_deg	1.264
r_mcangle_it	1.151
r_mcbond_it	0.614
r_symmetry_vdw_refined	0.194
r_nbd_refined	0.193
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
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	3976
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
AMoRE	phasing