4JEO | pdb_00004jeo

Crystal structure of red fluorescent protein lanRFPdam exposed to prolonged X-ray irradiation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HVF	PDB ENTRY 4HVF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	9 mg/ml of lanRFP in 20 mM Tris pH 8.0, 200 mM NaCl, 5 mM EDTA mixed with an equal amount of reservoir solution - 1M Na-citrate, 0.1M Tris pH 7.0 , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
3.96	68.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.274	α = 90
b = 134.274	β = 90
c = 156.851	γ = 120

Symmetry
Space Group	P 64 2 2

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	mirrors		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	2.34	30	98.7	0.131	7.2	5.6	31762	35065

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	2.34	2.42	99		0.627		5.7	3438

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 4HVF	2.35	29.83	33102	1340	93.27	0.1516	0.1497	0.1485	0.1981	0.1941	RANDOM	19.2455

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.135
r_dihedral_angle_4_deg	23.311
r_dihedral_angle_3_deg	16.279
r_dihedral_angle_1_deg	6.964
r_scangle_it	6.708
r_scbond_it	4.232
r_mcangle_it	2.479
r_angle_refined_deg	1.993
r_mcbond_it	1.311
r_chiral_restr	0.158
r_bond_refined_d	0.027
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3496
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing