X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VOFPDB ENTRY 2VOF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M SODIUM CITRATE (PH 5.6), 0.3 M (NH4)2SO4, 0.6 M LI2SO4
Crystal Properties
Matthews coefficientSolvent content
239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.239α = 90
b = 33.255β = 104.67
c = 58.508γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU IMAGE PLATEMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
11.930.6197.10.0719.14.7128911
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)
11.92950.462.94.7

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 2VOF1.930.611225863297.20.1850.1820.229RANDOM22.81
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]
0.431.070.22-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.564
r_dihedral_angle_4_deg22.632
r_dihedral_angle_3_deg14.912
r_dihedral_angle_1_deg5.199
r_scangle_it2.557
r_scbond_it1.779
r_angle_refined_deg1.089
r_mcangle_it1.014
r_angle_other_deg0.801
r_mcbond_it0.725
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.564
r_dihedral_angle_4_deg22.632
r_dihedral_angle_3_deg14.912
r_dihedral_angle_1_deg5.199
r_scangle_it2.557
r_scbond_it1.779
r_angle_refined_deg1.089
r_mcangle_it1.014
r_angle_other_deg0.801
r_mcbond_it0.725
r_nbd_refined0.21
r_symmetry_vdw_other0.201
r_nbtor_refined0.185
r_symmetry_vdw_refined0.177
r_nbd_other0.161
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.11
r_nbtor_other0.081
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1432
Nucleic Acid Atoms
Solvent Atoms122
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing