5VRD

Crystal structure for Methylobacterium extorquens PqqCD (natural fusion)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP292500 microL well volumes. Protein solution: 8.0 mg/mL protein, 50 mM Tris, pH 7.9, 100 mM sodium chloride, and 1 mM TCEP. Well solution: 100 mM HEPES, pH 6.7, 19% w/v PEG-4000, 10% isopropanol. Water used in the well solutions contained 0.55 mM sodium azide. Hanging drops were 1 microL protein solution and 1 microL well solution
Crystal Properties
Matthews coefficientSolvent content
2.957.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.936α = 90
b = 103.936β = 90
c = 243.485γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
12.85243.4998.50.0620.032174.531557

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1otv2.85243.4929899159398.380.25690.253140.32707RANDOM
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]
1.091.09-2.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.886
r_dihedral_angle_3_deg21.46
r_dihedral_angle_4_deg18.939
r_long_range_B_refined8.509
r_long_range_B_other8.503
r_dihedral_angle_1_deg8.119
r_mcangle_other5.641
r_mcangle_it5.64
r_scangle_other5.496
r_mcbond_it3.615
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.886
r_dihedral_angle_3_deg21.46
r_dihedral_angle_4_deg18.939
r_long_range_B_refined8.509
r_long_range_B_other8.503
r_dihedral_angle_1_deg8.119
r_mcangle_other5.641
r_mcangle_it5.64
r_scangle_other5.496
r_mcbond_it3.615
r_mcbond_other3.613
r_scbond_it3.444
r_scbond_other3.444
r_angle_refined_deg2.088
r_angle_other_deg1.241
r_chiral_restr0.119
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6570
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction