3CL1

M. loti cyclic-nucleotide binding domain, cyclic-GMP bound


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.346.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.202α = 90
b = 79.594β = 99.11
c = 49.984γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2004-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
1249.326870.0810.08123.315482
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)
22.1164.90.1550.15532.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.430.981524243993.40.2110.2090.256RANDOM16.16
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]
-0.35-0.580.79-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.69
r_dihedral_angle_4_deg18.457
r_dihedral_angle_3_deg15.917
r_dihedral_angle_1_deg5.438
r_scangle_it3.007
r_scbond_it1.668
r_angle_refined_deg1.309
r_mcangle_it0.929
r_mcbond_it0.464
r_symmetry_vdw_refined0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.69
r_dihedral_angle_4_deg18.457
r_dihedral_angle_3_deg15.917
r_dihedral_angle_1_deg5.438
r_scangle_it3.007
r_scbond_it1.668
r_angle_refined_deg1.309
r_mcangle_it0.929
r_mcbond_it0.464
r_symmetry_vdw_refined0.35
r_nbtor_refined0.302
r_nbd_refined0.241
r_xyhbond_nbd_refined0.182
r_symmetry_hbond_refined0.152
r_metal_ion_refined0.128
r_symmetry_metal_ion_refined0.078
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.003
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
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 Atoms1891
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms55

Software

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