4GW9 | pdb_00004gw9

Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	292	PROTEIN CONCENTRATION 20 MG/ML, 4% POLY-GAMMA-GLUTAMIC ACID POLYMER, 100 MM TRISHCL PH 8, 0.4 M NIACINAMIDE, 200 MM KBR, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.69	66.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.94	α = 90
b = 146.87	β = 101.17
c = 139.55	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 2M-F		2011-02-24	M	MAD
2	1	x-ray		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97911, 0.97949, 0.98244, 0.9700	Diamond	I03
2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
1,2	2.8	74	97.7	0.066	9.6	3.4		97789

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.8	2.87	96.4		0.63	1.4	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.9	15	83799	4419	97.71	0.20169	0.19952	0.2083	0.24318	0.2123	RANDOM	30.01

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]
-2.76		0.46	11.54		-8.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.646
r_dihedral_angle_3_deg	18.56
r_dihedral_angle_4_deg	16.756
r_dihedral_angle_1_deg	4.835
r_angle_refined_deg	2.523
r_angle_other_deg	1.323
r_chiral_restr	0.134
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19306
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms	172

Software

Software
Software Name	Purpose
GDA	data collection
SHARP	phasing
REFMAC	refinement
xia2	data reduction
XDS	data reduction
SCALA	data scaling