3N6Q

Crystal structure of YghZ from E. coli


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62930.2M MgFormate, 0.1M MES pH 6, 7.5% PEG 20,000, 4% 1,4 butanediol, VAPOR DIFFUSION, SITTING DROP, temperature 193K, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7254.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.7α = 90.27
b = 98.056β = 92.97
c = 98.257γ = 106.12
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rKOHZU: Double Crystal Si(111)2007-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11587ALS8.3.1

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
11.89896.70.060.0612.53.92943032943031124.7
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)
11.81.9950.5680.5682.23.942267

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2A791.894.071.32779251482496.20.170770.168750.2087RANDOM29.239
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]
-0.7-0.70.34-0.52-0.220.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.753
r_dihedral_angle_4_deg17.152
r_dihedral_angle_3_deg13.701
r_dihedral_angle_1_deg6.585
r_scangle_it5.876
r_scbond_it3.763
r_mcangle_it2.359
r_angle_refined_deg1.534
r_mcbond_it1.475
r_chiral_restr0.137
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.753
r_dihedral_angle_4_deg17.152
r_dihedral_angle_3_deg13.701
r_dihedral_angle_1_deg6.585
r_scangle_it5.876
r_scbond_it3.763
r_mcangle_it2.359
r_angle_refined_deg1.534
r_mcbond_it1.475
r_chiral_restr0.137
r_bond_refined_d0.019
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19673
Nucleic Acid Atoms
Solvent Atoms2642
Heterogen Atoms9

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling