2O9B | pdb_00002o9b

Crystal Structure of Bacteriophytochrome chromophore binding domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZTU	pdb entry 1ZTU without chromophore or his tag

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	0.095 M sodium citrate, 19% v/v isopropanol, 19% v/v PEG 4000, 5% V/V glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.5	α = 90
b = 51.5	β = 116.4
c = 80.8	γ = 90

Symmetry
Space Group	C 1 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	BRUKER PROTEUM	Bruker Montel mirrors	2005-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR

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	2.15	24	96.4	0.104	10	6.2	18137	17484		-3

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	2.15	2.23	78.8		0.333	2.7	2.6

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 (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 1ZTU without chromophore or his tag	2.15	23.71	17459	16539	920	96.5	0.1911	0.18852	0.19	0.23695	0.24	RANDOM	32.353

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]
-1.15		-0.12	0.76		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.565
r_dihedral_angle_4_deg	18.19
r_dihedral_angle_3_deg	14.453
r_dihedral_angle_1_deg	6.274
r_scangle_it	3.003
r_scbond_it	1.917
r_angle_refined_deg	1.806
r_mcangle_it	1.268
r_mcbond_it	0.796
r_nbtor_refined	0.3
r_symmetry_hbond_refined	0.249
r_symmetry_vdw_refined	0.217
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2394
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	43

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
HKL-2000	data reduction