3CGL | pdb_00003cgl

Crystal Structure and Raman Studies of dsFP483, a Cyan Fluorescent Protein from Discosoma striata

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1G7K	PDB code 1G7K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.9	277	100 mM HEPES pH 7.9, 300 mM NaCl, 200 mM calcium acetate, 16% v/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.202	α = 90
b = 78.269	β = 91.35
c = 188.566	γ = 90

Symmetry
Space Group	C 1 2 1

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	ADSC QUANTUM 4		2004-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.000	ALS	5.0.3

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	2.09	40	94.8	0.07	21.8	7		90778			16.4

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	2.1	2.18	67.5		0.359	5.4	5.1	6452

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 (All)	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 code 1G7K	2.09	40	86207	4569	94.81	0.18634	0.18476	0.21	0.21668	0.24	RANDOM	18.039

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]
-0.89		-0.62	2.57		-1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.314
r_dihedral_angle_3_deg	15.791
r_dihedral_angle_4_deg	15.651
r_dihedral_angle_1_deg	6.475
r_scangle_it	2.548
r_scbond_it	1.661
r_angle_refined_deg	1.52
r_mcangle_it	0.989
r_mcbond_it	0.514
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.314
r_dihedral_angle_3_deg	15.791
r_dihedral_angle_4_deg	15.651
r_dihedral_angle_1_deg	6.475
r_scangle_it	2.548
r_scbond_it	1.661
r_angle_refined_deg	1.52
r_mcangle_it	0.989
r_mcbond_it	0.514
r_nbtor_refined	0.307
r_symmetry_hbond_refined	0.276
r_metal_ion_refined	0.231
r_symmetry_vdw_refined	0.222
r_nbd_refined	0.207
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.093
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9060
Nucleic Acid Atoms
Solvent Atoms	567
Heterogen Atoms	2

Software

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

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.