6MGH | pdb_00006mgh

X-ray structure of monomeric near-infrared fluorescent protein miRFP670nano

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293	0.1M Na Acetate pH 4.0, 10mM EDTA, 10% isopropanol, 22% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.598	α = 90
b = 72.124	β = 129.99
c = 136.698	γ = 90

Symmetry
Space Group	C 1 2 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	RAYONIX MX300-HS		2018-01-01	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)	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	1.95	30	98.5	0.097	0.113	0.058	7.8	3.7		100484

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	1.95	2.02	97.6		0.557	0.661	0.353	0.762		3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.95	30	99377	1106	98.39	0.1831	0.1825	0.19	0.2392	0.25	RANDOM	26.903

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]
-0.61		-0.82	0.4		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.036
r_dihedral_angle_4_deg	22.769
r_dihedral_angle_3_deg	16.223
r_dihedral_angle_1_deg	7.381
r_angle_refined_deg	2.415
r_angle_other_deg	1.215
r_chiral_restr	0.147
r_bond_refined_d	0.019
r_gen_planes_other	0.015
r_gen_planes_refined	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.036
r_dihedral_angle_4_deg	22.769
r_dihedral_angle_3_deg	16.223
r_dihedral_angle_1_deg	7.381
r_angle_refined_deg	2.415
r_angle_other_deg	1.215
r_chiral_restr	0.147
r_bond_refined_d	0.019
r_gen_planes_other	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9697
Nucleic Acid Atoms
Solvent Atoms	584
Heterogen Atoms	376

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.