6YLQ | pdb_00006ylq

EGFP in neutral pH, Directionality of Optical Properties of Fluorescent Proteins

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	PEG 8000, HEPES, magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.94	α = 90
b = 62.12	β = 90
c = 68.86	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 300K		2019-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54187

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	39.39	86.5	0.077	0.084	0.999	15.35	5.924		24211			26.221

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.67	31.6		1.623	2.078	0.285	0.55	1.739

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	FOURIER SYNTHESIS	THROUGHOUT	1.65	39.39	22868	1204	89.29	0.1801	0.1782	0.19	0.2165	0.22	RANDOM	24.211

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]
0.04			-0.02		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.169
r_dihedral_angle_3_deg	13.285
r_dihedral_angle_4_deg	11.351
r_dihedral_angle_1_deg	6.962
r_angle_refined_deg	1.803
r_angle_other_deg	0.98
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.169
r_dihedral_angle_3_deg	13.285
r_dihedral_angle_4_deg	11.351
r_dihedral_angle_1_deg	6.962
r_angle_refined_deg	1.803
r_angle_other_deg	0.98
r_chiral_restr	0.099
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1807
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	474

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
REFMAC	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.