2ZOH

X-ray Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PHY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP, MICROSEEDING9295AMMONIUM SULPHATE, SODIUM CHLORIDE, SODIUM DIDEUTERIUM PHOSPHATE, DISODIUM DEUTERIUM PHOSPHATE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, MICROSEEDING, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.935.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.83α = 90
b = 66.83β = 90
c = 40.92γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295CCDADSC QUANTUM 3152006-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.45SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2557.831000.0580.05821.911.1289672896710.11
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.251.321000.3560.3567.311.34176

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R2PHY1.2550289502895014481000.11220.1488RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
101107
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.116
s_approx_iso_adps0.104
s_zero_chiral_vol0.08
s_similar_adp_cmpnt0.042
s_anti_bump_dis_restr0.031
s_angle_d0.03
s_from_restr_planes0.0289
s_bond_d0.013
s_rigid_bond_adp_cmpnt0.005
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1019
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms11

Software

Software
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
ADSCdata collection
XDSdata reduction
SCALAdata scaling
AMoREphasing