5I5L | pdb_00005i5l

The photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form, chromophore modelled with an endocyclic double bond in pyrrole ring A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5HSQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	16% PEG3350, 0.2 M CaCl2, 0.1 M Tris/HCl

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.019	α = 90
b = 173.019	β = 90
c = 78.823	γ = 90

Symmetry
Space Group	I 4 2 2

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 315r		2010-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9395	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.7	46.55	96.7	0.061	0.999	20	7.3		16105			62.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.85	87.7		0.64	3.3	6.1

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	5HSQ	2.7	46.55	15275	830	96.17	0.2187	0.21566	0.21	0.27901	0.28	RANDOM	77.119

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]
3.37			3.37		-6.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.991
r_dihedral_angle_4_deg	15.401
r_dihedral_angle_3_deg	15.251
r_dihedral_angle_1_deg	5.999
r_long_range_B_refined	4.544
r_long_range_B_other	4.522
r_mcangle_it	2.471
r_mcangle_other	2.471
r_scangle_other	2.368
r_angle_refined_deg	1.447
r_scbond_it	1.441
r_scbond_other	1.44
r_mcbond_it	1.432
r_mcbond_other	1.432
r_angle_other_deg	0.942
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3558
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
PHASER	phasing