5HSQ | pdb_00005hsq

The surface engineered 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	2VEA	2)9C, 2VEA (PHY domain)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.03 M diethyleneglycol, 0.03 M triethyleneglycol, 0.03 M tetraethyleneglycol, 0.03 M pentaethyleneglycol, 20% glycerol, 10% PEG8000, 0.05 M MES, 0.05 M imidazole pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.348	α = 90
b = 69.348	β = 90
c = 236.839	γ = 90

Symmetry
Space Group	P 43 21 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		2011-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.0718	ESRF	ID14-4

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	1.85	34.67	98.6	0.048	18.2	4.8	49518	49518			28.9

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	1.85	1.95	99.8		0.56	2.8	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2)9C, 2VEA (PHY domain)	1.85	34.31	46971	2528	97.96	0.18474	0.18269	0.19	0.22371	0.23	RANDOM	37.842

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]
-0.93			-0.93		1.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.889
r_sphericity_bonded	18.969
r_dihedral_angle_4_deg	16.785
r_dihedral_angle_3_deg	15.131
r_long_range_B_refined	7.405
r_long_range_B_other	7.355
r_dihedral_angle_1_deg	6.315
r_scangle_other	2.82
r_mcangle_it	2.231
r_mcangle_other	2.23
r_angle_refined_deg	2.048
r_scbond_it	1.867
r_scbond_other	1.867
r_mcbond_it	1.401
r_mcbond_other	1.398
r_angle_other_deg	1.15
r_chiral_restr	0.122
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3715
Nucleic Acid Atoms
Solvent Atoms	349
Heterogen Atoms	55

Software

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