2D1S

Crystal structure of the thermostable Japanese Firefly Luciferase complexed with High-energy intermediate analogue

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D1Q	PDB ENTRY 2D1Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.8	293	PEG4000, Lithium chrolide, Magnesium chloride, HEPES, 5'-O-[N-(dehydroluciferyl)-sulfamoyl] adenosine, pH 7.8, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.586	α = 90
b = 181.313	β = 90
c = 52.038	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	90	IMAGE PLATE	RIGAKU RAXIS V		2002-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.02	SPring-8	BL45XU

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	60	99.2	0.054	9	4	133611	133611	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)
	1.3	1.35	95.8		0.209	2.6	3.7	12734

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2D1Q	1.3	60	133504	126794	6710		0.18115	0.18115	0.18011	0.2008	RANDOM	11.684

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]
-0.19			-0.31		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.607
r_scangle_it	2.795
r_scbond_it	1.767
r_angle_refined_deg	1.371
r_mcangle_it	1.162
r_mcbond_it	0.639
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.166
r_chiral_restr	0.12
r_xyhbond_nbd_refined	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.607
r_scangle_it	2.795
r_scbond_it	1.767
r_angle_refined_deg	1.371
r_mcangle_it	1.162
r_mcbond_it	0.639
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.166
r_chiral_restr	0.12
r_xyhbond_nbd_refined	0.098
r_symmetry_hbond_refined	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4127
Nucleic Acid Atoms
Solvent Atoms	794
Heterogen Atoms	42

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.