4Z1W | pdb_00004z1w

CRYSTAL STRUCTURE OF MONOMERIC BACTERIOPHYTOCHROME mutant D207L Y263F From Synchrotron

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3S7Q	3S7Q, 4O8G
experimental model	PDB	4O8G	3S7Q, 4O8G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293	Crystals of D207L-Y263F phytochrome mutant were grown from hanging drop vapor diffusion in 20% PEG400, starting protein concentration of 20 mg/ml, and 0.1M phosphate citrate buffer at pH 4.0.

Crystal Properties
Matthews coefficient	Solvent content
2.23	46.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.434	α = 90
b = 53.34	β = 90.91
c = 65.69	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	MARMOSAIC 300 mm CCD		2015-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.9785	APS	21-ID-D

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	1.3	23.8	96.5	0.052	33.2	7.7		77741			8.8

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	1.3	1.35	94.3		0.35	1	7.7

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	3S7Q, 4O8G	1.3	23.22	73911	3829	96.36	0.14531	0.14455	0.15	0.16019	0.16	RANDOM	16.698

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]
-0.47		-0.71	0.59		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.835
r_sphericity_free	21.125
r_dihedral_angle_4_deg	12.679
r_dihedral_angle_3_deg	12.353
r_dihedral_angle_1_deg	6.383
r_sphericity_bonded	4.376
r_long_range_B_refined	1.778
r_long_range_B_other	1.479
r_angle_refined_deg	1.314
r_scangle_other	1.05
r_rigid_bond_restr	0.968
r_scbond_it	0.945
r_scbond_other	0.944
r_mcangle_it	0.884
r_mcangle_other	0.884
r_angle_other_deg	0.871
r_mcbond_it	0.752
r_mcbond_other	0.751
r_chiral_restr	0.069
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2389
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing