8OVY | pdb_00008ovy

Structure of analogue of superfolded GFP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B3P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	PEG 3350/PEG 1K/MPD (1:1:1) 37.5%, Bicine/Trizma 0.1 M pH 8.5, Morpheus III Alkaloids 0.8% w/v, Morpheus Alcohols 0.12 M

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.516	α = 90
b = 37.721	β = 106.376
c = 91.795	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	PIXEL	DECTRIS PILATUS3 2M		2023-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.84	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.537	88.071	93.1	0.11	0.99	5.1	3.3		59575

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.537	1.595			1.35	0.34

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.537	88.071	59575	2978	92.414	0.187	0.1858	0.2	0.2145	0.22	18.863

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]
-0.578		-0.501	0.539		0.284

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.34
r_dihedral_angle_3_deg	13.382
r_dihedral_angle_4_deg	10.163
r_dihedral_angle_1_deg	7.302
r_lrange_it	5.93
r_lrange_other	5.923
r_scangle_it	4.919
r_scangle_other	4.919
r_scbond_it	3.128
r_scbond_other	3.127
r_mcangle_it	2.407
r_mcangle_other	2.407
r_angle_refined_deg	1.789
r_mcbond_it	1.672
r_mcbond_other	1.669
r_angle_other_deg	1.406
r_nbd_refined	0.342
r_xyhbond_nbd_refined	0.24
r_symmetry_xyhbond_nbd_refined	0.233
r_symmetry_nbd_other	0.216
r_nbd_other	0.2
r_symmetry_nbd_refined	0.178
r_nbtor_refined	0.163
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3149
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	477

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing