4O01 | pdb_00004o01

Crystal Structure of D. radiodurans Bacteriophytochrome Photosensory Core Module in its Illuminated Form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O9C	PDB ENTRY 2O9C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.1M Tris, 0.2M NaCl, 25% PEG 3350, sequential 655nm illumination, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
4.23	70.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.9	α = 90
b = 195.7	β = 90
c = 225	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	PIXEL	DECTRIS PILATUS 6M-F		2013-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.98043	ESRF	ID23-1

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	3.24	49.22	99.9	0.241	0.248	9.69	19.31	61961	61928		-3	118.652

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	3.24	3.32	100		4.39	4.501	0.83	20.3	4495

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2O9C	3.24	49.22	61853	58759	3094	99.95	0.234	0.234	0.23265	0.225	0.25972	0.252	RANDOM	158.6115

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]
5.55			-1.75		-3.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.587
r_dihedral_angle_3_deg	15.249
r_dihedral_angle_4_deg	10.871
r_mcangle_it	9.369
r_mcbond_it	5.78
r_mcbond_other	5.778
r_dihedral_angle_1_deg	5.402
r_angle_refined_deg	1.159
r_angle_other_deg	0.703
r_chiral_restr	0.052
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14784
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	172

Software

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