4Q7R | pdb_00004q7r

Crystal structure of large Stokes shift fluorescent protein LSSmOrange

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H5O	PDB ENTRY 2H5O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	0.2 M zinc acetate, 0.1 M acetate buffer, 20% PEG1000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.436	α = 90
b = 107.364	β = 102.15
c = 56.602	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 300 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	1.4	55.335	98.6	0.056	10	4.2		84546

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	1.4	1.45	97.1		0.628		4.1	8345

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2H5O	1.4	55.33	84451	1687	98.48	0.1479	0.1473	0.1748	0.1753	RANDOM	18.796

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]
-0.28		-0.07	-0.1		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.922
r_sphericity_free	19.134
r_dihedral_angle_3_deg	13.939
r_dihedral_angle_4_deg	11.529
r_sphericity_bonded	9.686
r_dihedral_angle_1_deg	6.445
r_rigid_bond_restr	5.91
r_angle_refined_deg	1.977
r_chiral_restr	0.159
r_bond_refined_d	0.014
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3549
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	53

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
DENZO	data reduction
MOLREP	phasing