4MRA

Crystal structure of Gpb in complex with QUERCETIN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SYMpdb entry 3SYM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES6.728910mM BES buffer, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4750.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.6α = 90
b = 126.6β = 90
c = 115.821γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDMAR CCD 165 mm2013-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.34301000.101189.94039940399-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.342.381000.461510

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-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpdb entry 3SYM2.3429.233826538265202399.650.181960.178660.190.243950.25RANDOM30.332
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]
-0.06-0.060.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.391
r_dihedral_angle_4_deg20.955
r_dihedral_angle_3_deg17.341
r_dihedral_angle_1_deg6.782
r_mcangle_it3.393
r_scbond_it2.85
r_mcbond_it2.188
r_mcbond_other2.184
r_angle_refined_deg1.616
r_angle_other_deg0.895
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6578
Nucleic Acid Atoms
Solvent Atoms352
Heterogen Atoms26

Software

Software
Software NamePurpose
DNAdata collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing