3MGF | pdb_00003mgf

Crystal Structure of Monomeric Kusabira-Orange (MKO), Orange-Emitting GFP-like Protein, at pH 7.5

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2M L-Proline, 0.1M HEPES, 10%(w/v) Polyethylene glycol 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.52	α = 90
b = 83.76	β = 110.75
c = 82.18	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	ADSC QUANTUM 210		2009-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	1.8	20	99.5	0.06	23.79			79034

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	PDB entry 2ZMW	1.8	19.78	79012	3963	99.68	0.169	0.166	0.17	0.213	0.21	RANDOM	17.364

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]
-0.09		-0.04	0.04		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.726
r_dihedral_angle_4_deg	19.866
r_dihedral_angle_3_deg	14.741
r_dihedral_angle_1_deg	6.986
r_scangle_it	5.538
r_scbond_it	3.579
r_mcangle_it	2.138
r_angle_refined_deg	2.115
r_mcbond_it	1.281
r_chiral_restr	0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.726
r_dihedral_angle_4_deg	19.866
r_dihedral_angle_3_deg	14.741
r_dihedral_angle_1_deg	6.986
r_scangle_it	5.538
r_scbond_it	3.579
r_mcangle_it	2.138
r_angle_refined_deg	2.115
r_mcbond_it	1.281
r_chiral_restr	0.17
r_bond_refined_d	0.024
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6787
Nucleic Acid Atoms
Solvent Atoms	851
Heterogen Atoms

Software

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