3PYP

PHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT CYCLE INTERMEDIATE


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.8pH 4.8
Crystal Properties
Matthews coefficientSolvent content
1.832

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.224α = 90
b = 66.224β = 90
c = 40.561γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray149IMAGE PLATEMARRESEARCHMIRRORS1997-09-06M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-1SSRLBL9-1

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
10.8597.70.0420.04210.96.684934
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)
0.850.8687.10.520.521.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAME CRYSTAL LATTICE MOLECULAR REPLACEMENTFREE R-VALUE2PHY0.855080680424997.70.13260.15485% RANDOMLY CHOSEN BY SHELX
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
189431133
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.112
s_zero_chiral_vol0.098
s_anti_bump_dis_restr0.064
s_angle_d0.038
s_bond_d0.017
s_similar_dist
s_from_restr_planes
s_rigid_bond_adp_cmpnt
s_similar_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1094
Nucleic Acid Atoms
Solvent Atoms196
Heterogen Atoms11

Software

Software
Software NamePurpose
SHELX-97refinement
DENZOdata reduction
SCALEPACKdata scaling