2YDZ | pdb_00002ydz

X-ray structure of the cyan fluorescent protein SCFP3A (K206A mutant)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.75		16 MG/ML PROTEIN, 13% PEG8000, 100 MM MGCL2, 100 MM HEPES PH 6.75

Crystal Properties
Matthews coefficient	Solvent content
2	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.146	α = 90
b = 62.14	β = 90
c = 69.781	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	100	CCD	ADSC CCD	TOROIDAL MIRROR	2010-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	1.59	46.4	96.1	0.06	14.8	4		29189		2

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	1.59	1.68	95.6		0.83	2	4

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2WSO	1.59	46.41	27687	1476	95.42	0.1445	0.1419	0.15	0.19328	0.2	RANDOM	19.736

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]
-0.46			0.1		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.736
r_sphericity_free	23.601
r_dihedral_angle_3_deg	13.149
r_sphericity_bonded	9.996
r_dihedral_angle_4_deg	8.422
r_dihedral_angle_1_deg	6.57
r_rigid_bond_restr	2.827
r_angle_refined_deg	1.41
r_angle_other_deg	0.795
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1804
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing