5VIK | pdb_00005vik

Crystal structure of monomeric near-infrared fluorescent protein miRFP703

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.08M Na Citrate pH 5.0, 24% v/v Jeffamine ED-2001 pH 7.0 0.4% n-octyl-beta-D-glucopyranoside

Crystal Properties
Matthews coefficient	Solvent content
1.79	31.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.319	α = 90
b = 52.821	β = 92.53
c = 64.622	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 225 mm CCD		2016-12-01	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.35	29.93	99.9	0.054	0.063	0.033	13.6	3.7		53575

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.4	99.9		0.368	0.441	0.241	0.868		3.3

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	4XTQ	1.35	29.93	51889	1666	99.83	0.1232	0.1215	0.12	0.174	0.17	RANDOM	20.485

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]
1.39		-1.03	-1.63		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.794
r_sphericity_free	23.238
r_dihedral_angle_4_deg	17.884
r_dihedral_angle_3_deg	13.517
r_sphericity_bonded	12.354
r_rigid_bond_restr	7.343
r_dihedral_angle_1_deg	7.026
r_angle_refined_deg	2.324
r_angle_other_deg	1.448
r_chiral_restr	0.129
r_bond_refined_d	0.022
r_gen_planes_other	0.017
r_gen_planes_refined	0.013
r_bond_other_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2299
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	43

Software

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