2QU1 | pdb_00002qu1

Crystal Structure of a Cyclized GFP Variant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G6E	PDB entry 2G6E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	Protein solution (4.95 mg/ml Protein, 0.050 M Sodium chloride, 0.0003 M TCEP, 0.005 M Bis-Tris pH 7.0) mixed in a 1:1 ratio with the Well solution (0.080 M Calcium chloride, 15% PEG 4000, 0.1 M HEPPS pH 8.5) and cryoprotected with well solution supplemented with 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.2	42.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.46	α = 90
b = 61.99	β = 90
c = 70.02	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	BRUKER PROTEUM-R	MONTEL OPTICS	2007-04-01		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	1.7	70.2	99	0.0976	28.27	29.45		25086

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)
	1.7	1.75	96.8		0.6834	2.93	5.42	2000

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 2G6E	1.7	46.424	25028	1276	98.98	0.171	0.168	0.1721	0.22	0.2236	RANDOM	12.341

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]
0.312			-0.42		0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.293
r_dihedral_angle_3_deg	12.058
r_dihedral_angle_4_deg	11.385
r_dihedral_angle_1_deg	6.337
r_scangle_it	3.52
r_scbond_it	2.291
r_angle_refined_deg	1.548
r_mcangle_it	1.285
r_mcbond_it	0.866
r_nbtor_refined	0.303
r_nbd_refined	0.235
r_symmetry_hbond_refined	0.23
r_symmetry_metal_ion_refined	0.194
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.096
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1915
Nucleic Acid Atoms
Solvent Atoms	377
Heterogen Atoms	1

Software

Software
Software Name	Purpose
SAINT	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	data reduction
SADABS	data scaling