1ZTU | pdb_00001ztu

Structure of the chromophore binding domain of bacterial phytochrome

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.95	298	PEG 400, sodium acetate, pH 4.95, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.244	62.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.876	α = 90
b = 133.666	β = 90
c = 49.938	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	98	CCD	MARRESEARCH		2004-10-25	M	MAD
2	1	x-ray	98	CCD	MARRESEARCH		2004-10-25	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 32-ID	0.9793, 0.9791	APS	32-ID
2	SYNCHROTRON	APS BEAMLINE 32-ID	0.9793, 0.9791	APS	32-ID

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	2.5	30	97	0.056	14.2	6.7		15209

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)
	2.5	2.59	90.4		0.111	10.8	5.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.5	20	15154	14403	751	97.08	0.23887	0.23746	0.29	0.26569	0.32	RANDOM	48.759

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]
-7.09			-8.42		15.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.562
r_dihedral_angle_3_deg	19.545
r_dihedral_angle_4_deg	17.551
r_dihedral_angle_1_deg	6.608
r_scangle_it	1.944
r_angle_refined_deg	1.817
r_scbond_it	1.153
r_mcangle_it	0.767
r_mcbond_it	0.429
r_symmetry_vdw_refined	0.376
r_nbtor_refined	0.301
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.103
r_symmetry_hbond_refined	0.101
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
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	2408
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	43

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction