4LC1

MeaB, A Bacterial Homolog of MMAA, Bound to GDP and crystallized in the presence of GDP and [AlF4]-


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QM7PDB ENTRY 2QM7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529320 % (w/v) PEG3350, and 0.2 M sodium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3246.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.667α = 90
b = 78.623β = 108.61
c = 69.622γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDK-B pair of biomorph mirrors for vertical and horizontal focusing2008-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.03262APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.85099.56039560064
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)
11.81.9197.70.3930.4034.434.29832

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2QM71.847.896022757038302699.730.1960.181270.179340.21652RANDOM27.253
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]
0.650.48-1.381.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.787
r_dihedral_angle_4_deg16.995
r_dihedral_angle_3_deg12.887
r_dihedral_angle_1_deg5.312
r_angle_other_deg2.981
r_angle_refined_deg1.483
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.787
r_dihedral_angle_4_deg16.995
r_dihedral_angle_3_deg12.887
r_dihedral_angle_1_deg5.312
r_angle_other_deg2.981
r_angle_refined_deg1.483
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4613
Nucleic Acid Atoms
Solvent Atoms460
Heterogen Atoms62

Software

Software
Software NamePurpose
Blu-Icedata collection
EPMRphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling