X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
172.9M SODIUM MALONATE, PH 7
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.77α = 90
b = 47.77β = 90
c = 83.36γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORSMMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.954, 1.907ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.541.3898.60.0511.585.1117909217.636
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)
11.51.5893.20.481.64.06

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 DIFFRACTIONMADTHROUGHOUTNONE1.541.381703387598.450.176610.174860.2102RANDOM16.761
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]
0.130.070.13-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.088
r_dihedral_angle_3_deg13.926
r_dihedral_angle_4_deg8.453
r_scangle_it6.736
r_dihedral_angle_1_deg5.137
r_scbond_it4.238
r_mcangle_it2.605
r_rigid_bond_restr1.741
r_angle_refined_deg1.652
r_mcbond_it1.602
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.088
r_dihedral_angle_3_deg13.926
r_dihedral_angle_4_deg8.453
r_scangle_it6.736
r_dihedral_angle_1_deg5.137
r_scbond_it4.238
r_mcangle_it2.605
r_rigid_bond_restr1.741
r_angle_refined_deg1.652
r_mcbond_it1.602
r_angle_other_deg1.012
r_mcbond_other0.523
r_chiral_restr0.096
r_bond_refined_d0.017
r_bond_other_d0.012
r_gen_planes_refined0.007
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms802
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms9

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
SHELXDphasing
SHARPphasing
REFMACrefinement