2D02 | pdb_00002d02

R52Q Mutant of 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	293	40% PEG2000, 100mM sodium citrate, pH 6.0, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.9	33.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.02	α = 90
b = 37.02	β = 90
c = 129.62	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	2004-01-01	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	1.42	25.74	99.9	0.07	17	11.1		18879

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	1.42	20	17895	971	99.95	0.1418	0.1406	0.14	0.16346	0.13	RANDOM	13.247

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]
0.22	0.11		0.22		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.164
r_dihedral_angle_4_deg	14.554
r_dihedral_angle_3_deg	12.321
r_dihedral_angle_1_deg	5.899
r_sphericity_free	5.017
r_scangle_it	4.012
r_sphericity_bonded	3.235
r_scbond_it	2.811
r_mcangle_it	2.082
r_rigid_bond_restr	1.537
r_mcbond_it	1.51
r_angle_refined_deg	1.494
r_nbtor_refined	0.311
r_nbd_refined	0.248
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.181
r_symmetry_hbond_refined	0.163
r_chiral_restr	0.105
r_bond_refined_d	0.013
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	999
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	11

Software

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