X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829850 mM TRIS pH, 100 mM NaCl, 20 mM ZnCl, 20 mM Cyanocobalamin, PEG2000 20%
Crystal Properties
Matthews coefficientSolvent content
2.5752.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.177α = 90
b = 100.593β = 97.6
c = 79.579γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
1278.89990.9614851840
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1280.94

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6FFV244.19951786253199.8960.1840.1810.2432RANDOM29.056
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]
4.3051.984-3.026-1.747
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.588
r_dihedral_angle_3_deg14.227
r_dihedral_angle_2_deg12.888
r_dihedral_angle_1_deg7.763
r_rigid_bond_restr3.988
r_lrange_it3.824
r_lrange_other3.823
r_scangle_it2.817
r_scangle_other2.817
r_mcangle_it2.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.588
r_dihedral_angle_3_deg14.227
r_dihedral_angle_2_deg12.888
r_dihedral_angle_1_deg7.763
r_rigid_bond_restr3.988
r_lrange_it3.824
r_lrange_other3.823
r_scangle_it2.817
r_scangle_other2.817
r_mcangle_it2.46
r_mcangle_other2.46
r_scbond_it2.068
r_scbond_other2.068
r_angle_refined_deg1.806
r_mcbond_it1.703
r_mcbond_other1.689
r_angle_other_deg0.778
r_nbd_other0.261
r_symmetry_nbd_refined0.239
r_symmetry_nbd_other0.176
r_nbtor_refined0.174
r_nbd_refined0.168
r_symmetry_xyhbond_nbd_refined0.149
r_chiral_restr0.135
r_xyhbond_nbd_refined0.124
r_symmetry_nbtor_other0.081
r_ncsr_local_group_10.071
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5247
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms331

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing