3DQD

Structure of the Yellow Fluorescent Protein Citrine Frozen at 1250 Atmospheres Number 2: Structure 12 in a Series of 26 High Pressure Structures

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HUY	PDB ENTRY 1HUY WITH RESIDUE 80 MUTATED TO GLUTAMINE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	277	Crystals grown by seeding using a Seed Bead (HR2-320, Hampton Research) in 5% PEG 3350, 50 mM Na Acetate, 50 mM NH4 Acetate, pH 5.0. Crystals were grown at 4 deg C and at ambient pressure, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.193	α = 90
b = 62.977	β = 90
c = 71.128	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	CCD	ADSC QUANTUM 210		2005-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F2	0.9795	CHESS	F2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.4	39.72	59.3	0.064	0.064	10.3	4.6		27256

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.4		100		0.303	0.303	2.5	4.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1HUY WITH RESIDUE 80 MUTATED TO GLUTAMINE	1.4	20	25884	1355	59.31	0.21605	0.21271	0.28004	RANDOM	27.484

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]
-0.06			-0.09		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.629
r_dihedral_angle_3_deg	17.993
r_dihedral_angle_4_deg	13.143
r_dihedral_angle_1_deg	7.212
r_scangle_it	5.592
r_scbond_it	3.856
r_angle_refined_deg	2.251
r_mcangle_it	2.116
r_mcbond_it	1.812
r_nbtor_refined	0.306
r_nbd_refined	0.262
r_symmetry_vdw_refined	0.215
r_symmetry_hbond_refined	0.214
r_xyhbond_nbd_refined	0.186
r_chiral_restr	0.15
r_bond_refined_d	0.025
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1850
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DPS	data reduction