2F8P | pdb_00002f8p

Crystal structure of obelin following Ca2+ triggered bioluminescence suggests neutral coelenteramide as the primary excited state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SL7	PDB ENTRY 1SL7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	277	2% PEG 400, 2.0 M ammonium sulfate, 0.1 M HEPES-Na , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.26	α = 90
b = 64.26	β = 90
c = 63.049	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	CCD	MARRESEARCH		2005-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.87	64.28	80.3	0.069	0.075	25	5.2		17133		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.86	1.93	17.3		0.26	0.26	1.66	1.4

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 (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 1SL7	1.93	28.74	17133	15977	844	86.71	0.1924	0.19043	0.19	0.22997	0.19	RANDOM	28.128

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.97
r_dihedral_angle_4_deg	21.043
r_dihedral_angle_3_deg	15.102
r_dihedral_angle_1_deg	5.545
r_scangle_it	4.243
r_scbond_it	2.681
r_mcangle_it	1.621
r_angle_refined_deg	1.461
r_mcbond_it	0.936
r_nbtor_refined	0.302
r_nbd_refined	0.218
r_symmetry_vdw_refined	0.202
r_symmetry_hbond_refined	0.195
r_xyhbond_nbd_refined	0.18
r_metal_ion_refined	0.162
r_chiral_restr	0.113
r_bond_refined_d	0.016
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	1529
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing