1UWN | pdb_00001uwn

The Initial Events in the Photocycle of Photoactive Yellow Protein: A Common Mechanism on Light Activation in Photoreceptor Proteins

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	2.25 M NH4SO4, 20 MM SODIUM PHOSPHATE PH 7, VAPOR DIFFUSION, HANGING DROP, TEMP 298K

Crystal Properties
Matthews coefficient	Solvent content
1.72	20

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.922	α = 90
b = 65.922	β = 90
c = 40.584	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	85	CCD	ADSC CCD	BENT MIRROR	2002-03-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9393, 0.9796	ESRF	ID14-4

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	1.2	30	98.1	0.033	15.9	5.2		159748		-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	1.2	1.23	92.4		0.171	5.5	3.5

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.2	40	29290	1559	98.1	0.125	0.124	0.147	RANDOM	10.96

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]
-0.16	-0.08		-0.16		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.508
r_scangle_it	4.288
r_scbond_it	2.932
r_mcangle_it	2.234
r_angle_refined_deg	1.83
r_angle_other_deg	1.66
r_mcbond_it	1.469
r_symmetry_vdw_other	0.281
r_nbd_refined	0.279
r_symmetry_hbond_refined	0.266
r_nbd_other	0.264
r_symmetry_vdw_refined	0.224
r_nbtor_other	0.176
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.114
r_bond_refined_d	0.019
r_gen_planes_other	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	970
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHARP	phasing