4RQ9 | pdb_00004rq9

Crystal structure of the chromophore-binding domain of Stigmatella aurantiaca bacteriophytochrome (Thr289His mutant) in the Pr state

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	289	protein: 25-28 mg ml-1 in 10 mM Tris HCl (pH 8.0) and 10 mM NaCl. crystallization conditions: 260 mM potassium sodium tartrate tetrahydrate, 35% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
6.28	80.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.813	α = 90
b = 131.813	β = 90
c = 97.218	γ = 120

Symmetry
Space Group	P 32 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	ADSC QUANTUM 315r	mirror	2011-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97926	APS	19-ID

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	2.5	30	99.9	0.085	19.3	7	33975	33975		-3	66

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	2.5	2.54	100		0.543	3.7	7.1	1682

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	PDB entry 4RPW	2.5	29.96	32204	1738	99.63	0.1566	0.15546	0.1582	0.17776	0.1794	RANDOM	56.772

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]
-0.43	-0.43		-0.43		1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.794
r_dihedral_angle_4_deg	17.566
r_dihedral_angle_3_deg	12.833
r_dihedral_angle_1_deg	3.682
r_angle_refined_deg	1.858
r_angle_other_deg	1.619
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2392
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	147

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling