6M9Y | pdb_00006m9y

X-ray Structure of Branchiostoma floridae fluorescent protein lanFP6A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HVF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.2M Ammonium Citrate pH 7.0, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.726	α = 90
b = 98.169	β = 108.07
c = 55.145	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	MARMOSAIC 225 mm CCD		2018-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

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	1.35	30	93.7	0.044	0.053	0.029	10.2	2.4		116582

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	1.35	1.4	90.5		0.537	0.684	0.418	0.731		2.4

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	4HVF	1.35	28.03	106408	1079	86.34	0.1333	0.133	0.1354	0.1688	0.17	RANDOM	19.371

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]
0.02		0.07	-0.46		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.013
r_sphericity_free	25.646
r_dihedral_angle_4_deg	15.396
r_dihedral_angle_3_deg	13.569
r_sphericity_bonded	12.556
r_dihedral_angle_1_deg	7.254
r_rigid_bond_restr	3.45
r_angle_refined_deg	1.723
r_angle_other_deg	1.03
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3512
Nucleic Acid Atoms
Solvent Atoms	609
Heterogen Atoms

Software

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