Experiment: 9AZ9

Chloride Sites in Photoactive Yellow Protein (Chloride-Free Reference Structure)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		wt63rt_new.pdb 2005-05-18

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	2.5 M ammonium sulfate, 1.5 M sodium chloride, 20 mM sodium phosphate, dialyzed against (1) 3.0 M ammonium sulfate, 0.5 M sodium chloride, 20 mM sodium phosphate, then (2) 3.5 M ammonium sulfate, 20 mM sodium phosphate

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.89	α = 90
b = 66.89	β = 90
c = 40.93	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	293	CCD	RIGAKU SATURN A200		2012-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	21.89	97.2	0.022	0.024	1	50	5.5		13465			13.85

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	79.1		0.038	0.997		5.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	21.89	2.23	13460	1332	97.25	0.1399	0.1358	0.1361	0.1759	0.1758	18.19

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.4672
f_angle_d	0.8598
f_chiral_restr	0.0583
f_bond_d	0.0062
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	975
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	11

Software

Software
Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction