4ZIN | pdb_00004zin

Genetically encoded Phenyl Azide Photochemistry Drive Positive and Negative Functional Modulation of a Red Fluorescent Protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H5O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	291	Sitting drop

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.28	α = 90
b = 103.43	β = 90
c = 150.72	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 6M		2014-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97623	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	1.67	51.71	100	0.074	0.03	0.998	13.6	7.1		79561

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.67	1.71	100		0.814	0.324	0.772	2.4	7.2	5770

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	2H5O	1.67	51.71	75603	3874	99.93	0.208	0.2059	0.21	0.2476	0.25	RANDOM	29.43

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]
-2.38			0.01		2.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.869
r_dihedral_angle_4_deg	19.358
r_dihedral_angle_3_deg	14.841
r_dihedral_angle_1_deg	7.097
r_mcangle_it	2.471
r_angle_refined_deg	2.12
r_mcbond_it	1.839
r_mcbond_other	1.829
r_angle_other_deg	0.925
r_chiral_restr	0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.869
r_dihedral_angle_4_deg	19.358
r_dihedral_angle_3_deg	14.841
r_dihedral_angle_1_deg	7.097
r_mcangle_it	2.471
r_angle_refined_deg	2.12
r_mcbond_it	1.839
r_mcbond_other	1.829
r_angle_other_deg	0.925
r_chiral_restr	0.14
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5235
Nucleic Acid Atoms
Solvent Atoms	400
Heterogen Atoms	34

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHASER	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.