1S36 | pdb_00001s36

Crystal structure of a Ca2+-discharged photoprotein: Implications for the mechanisms of the calcium trigger and the bioluminescence

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JF2	PDB ENTRY 1JF2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	modified microbatch	7.5	277	1.5 M tri-sodium citrate, 0.1 M Na-HEPES, pH 7.5, modified microbatch, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.445	α = 90
b = 53.445	β = 90
c = 144.032	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	BRUKER SMART 6000	Rigaku/msc HiRes2	2002-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	1.96	72.46	1	0.06	9.37	14.91		15775		-3	15

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.96	2.05	0.97		0.19	2.11		1982

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1JF2	1.96	50	14823	780	98.51	0.22459	0.22278	0.25922	RANDOM	16.388

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]
0.42			0.42		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.924
r_scangle_it	3.421
r_scbond_it	2.156
r_mcangle_it	1.288
r_angle_refined_deg	1.207
r_mcbond_it	0.698
r_symmetry_vdw_refined	0.214
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.172
r_symmetry_hbond_refined	0.162
r_metal_ion_refined	0.133
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
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_other
r_symmetry_vdw_other
r_symmetry_hbond_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	1489
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
LSCALE	data scaling