3I19 | pdb_00003i19

1.4 Angstrom Crystal Structure of Fluorescent Protein Cypet

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	30% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.873	α = 90
b = 63.02	β = 90
c = 71.078	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	MARMOSAIC 225 mm CCD		2009-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	1.0082	SSRF	BL17U

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	1.36	50	99	0.047	0.042	41	5.8		49295	2	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)
	1.36	1.38	91.6		0.194	0.201	6.1	4.5	2238

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1QYO	1.36	29.14	2	2	46743	2489	98.96	0.1731	0.16907	0.16759	0.1821	0.19693	0.1911	RANDOM	15.314

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			-0.49		0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.842
r_dihedral_angle_3_deg	10.496
r_dihedral_angle_4_deg	8.413
r_dihedral_angle_1_deg	6.606
r_angle_refined_deg	1.164
r_nbtor_refined	0.319
r_nbd_refined	0.254
r_symmetry_vdw_refined	0.173
r_xyhbond_nbd_refined	0.156
r_symmetry_hbond_refined	0.14
r_chiral_restr	0.073
r_bond_refined_d	0.004
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1870
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling