7X2B | pdb_00007x2b

Red fluorescent protein from Diadumene lineata

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VK1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	3.0 M Ammonium Sulfate, 0.1 M Immidazole, 2.5 mg/mL protein

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.929	α = 90
b = 75.394	β = 90
c = 118.955	γ = 90

Symmetry
Space Group	I 2 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	PIXEL	DECTRIS PILATUS3 S 6M		2021-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

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	1.63	43.65	100	0.068	13	6.6		26779

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	1.63	1.66			0.788	2.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3vk1	1.63	20.001	26766	1398	99.866	0.173	0.1711	0.18	0.2054	0.21	23.948

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]
3.036			0.328		-3.364

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.063
r_dihedral_angle_4_deg	17.302
r_dihedral_angle_3_deg	14.127
r_dihedral_angle_1_deg	7.304
r_lrange_it	4.942
r_lrange_other	4.904
r_scangle_it	4.135
r_scangle_other	4.129
r_scbond_it	2.829
r_scbond_other	2.827
r_mcangle_it	2.404
r_mcangle_other	2.403
r_mcbond_it	1.817
r_mcbond_other	1.817
r_angle_refined_deg	1.674
r_angle_other_deg	1.37
r_nbd_refined	0.264
r_symmetry_nbd_refined	0.261
r_nbd_other	0.255
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.117
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1742
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHENIX	refinement