4O0P | pdb_00004o0p

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

X-RAY DIFFRACTION

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	7	298	30% PEG 1500, in dark, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
4.2	70.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.28	α = 90
b = 150.28	β = 90
c = 145.95	γ = 120

Symmetry
Space Group	P 64

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	0.98044	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	3.8	48.65	99.9	0.392	0.411	4.72	10.97	18561	18551		-3	130.975

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.8	3.9	100		4.513	4.725	4.725	1.05	11.6	1362

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	3.8	48.65	18525	17597	928	99.92	0.2536	0.2536	0.2529	0.23	0.2657	0.25	RANDOM	210.2428

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]
-1.8			-1.8		3.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.656
r_mcangle_it	19.206
r_dihedral_angle_3_deg	14.352
r_mcbond_other	11.632
r_mcbond_it	11.631
r_dihedral_angle_4_deg	10.009
r_dihedral_angle_1_deg	5.42
r_angle_refined_deg	1.112
r_angle_other_deg	0.727
r_chiral_restr	0.051

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.656
r_mcangle_it	19.206
r_dihedral_angle_3_deg	14.352
r_mcbond_other	11.632
r_mcbond_it	11.631
r_dihedral_angle_4_deg	10.009
r_dihedral_angle_1_deg	5.42
r_angle_refined_deg	1.112
r_angle_other_deg	0.727
r_chiral_restr	0.051
r_bond_refined_d	0.006
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	7416
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	86

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.