1Z9T

CRYSTAL STRUCTURE OF A PUTATIVE LACCASE (YFIH) FROM ESCHERICHIA COLI AT 1.54 A RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U05 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP52770.2M (NH4)2HCitrate, 20.0% PEG-3350, No Buffer pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4749.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.711α = 90
b = 80.711β = 90
c = 90.589γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)2005-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-1SSRLBL9-1

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
11.5460.31000.0796.76.844917
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)
11.541.581000.75817

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1u051.5460.342591226299.950.1430.143240.1420.172RANDOM17.354
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]
-0.57-0.571.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.249
r_dihedral_angle_4_deg17.24
r_dihedral_angle_3_deg11.755
r_scangle_it6.193
r_dihedral_angle_1_deg5.88
r_scbond_it4.358
r_mcangle_it2.437
r_mcbond_it2.004
r_angle_refined_deg1.732
r_angle_other_deg1.447
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.249
r_dihedral_angle_4_deg17.24
r_dihedral_angle_3_deg11.755
r_scangle_it6.193
r_dihedral_angle_1_deg5.88
r_scbond_it4.358
r_mcangle_it2.437
r_mcbond_it2.004
r_angle_refined_deg1.732
r_angle_other_deg1.447
r_mcbond_other0.474
r_symmetry_vdw_other0.238
r_symmetry_hbond_refined0.238
r_nbd_refined0.211
r_nbd_other0.189
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.143
r_symmetry_vdw_refined0.142
r_chiral_restr0.098
r_nbtor_other0.086
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1799
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing