2D01 | pdb_00002d01

Wild Type Photoactive Yellow Protein, P65 Form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PHY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	40% PEG2000, 100mM sodium citrate, pH 6.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2	38.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.422	α = 90
b = 40.422	β = 90
c = 118.131	γ = 120

Symmetry
Space Group	P 65

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	ADSC QUANTUM 4	bending magnet	2004-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL40B2	1.000	SPring-8	BL40B2

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	1.34	20.09	99.8	0.053	14.2	11.1		23170

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)
	1.34	1.39	99.8		0.303	9.09	11

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	2PHY	1.34	20	23170	1244	99.91	0.15397	0.15209	0.15	0.18915	0.15	RANDOM	16.989

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]
0.53	0.27		0.53		-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.474
r_dihedral_angle_3_deg	15.769
r_dihedral_angle_4_deg	12.98
r_dihedral_angle_1_deg	6.074
r_sphericity_free	5.36
r_sphericity_bonded	4.264
r_scangle_it	3.615
r_scbond_it	2.857
r_mcangle_it	2.289
r_rigid_bond_restr	2.094
r_mcbond_it	1.596
r_angle_refined_deg	1.487
r_nbtor_refined	0.316
r_nbd_refined	0.257
r_symmetry_vdw_refined	0.21
r_xyhbond_nbd_refined	0.185
r_symmetry_hbond_refined	0.164
r_chiral_restr	0.102
r_bond_refined_d	0.012
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1025
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	11

Software

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