3GEH

Crystal structure of MnmE from Nostoc in complex with GDP, FOLINIC ACID and ZN


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5293100mM TRIS-HCl, pH 7.5, 22% (w/v) PEG 550 MME, 10mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
6.73061181.725288

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.279α = 90
b = 124.279β = 90
c = 174.701γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2007-08-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.28186SLSX10SA

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
13.22099.40.1270.1788.617.8232502310076.546
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.399.90.4852.188.032004

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1XZP3.219.9921913118699.910.241920.240530.26743RANDOM52.543
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]
1.091.09-2.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.203
r_dihedral_angle_3_deg20.574
r_dihedral_angle_4_deg16.015
r_dihedral_angle_1_deg5.696
r_angle_refined_deg1.185
r_scangle_it0.919
r_mcangle_it0.704
r_scbond_it0.493
r_mcbond_it0.388
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.203
r_dihedral_angle_3_deg20.574
r_dihedral_angle_4_deg16.015
r_dihedral_angle_1_deg5.696
r_angle_refined_deg1.185
r_scangle_it0.919
r_mcangle_it0.704
r_scbond_it0.493
r_mcbond_it0.388
r_nbtor_refined0.295
r_nbd_refined0.203
r_symmetry_vdw_refined0.17
r_xyhbond_nbd_refined0.114
r_chiral_restr0.082
r_symmetry_hbond_refined0.071
r_bond_refined_d0.007
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3364
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms64

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling