X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V23PDB ENTRY 2V23

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS6MICRODIALYSIS AGAINST 30% MPD., pH 6.0
Crystal Properties
Matthews coefficientSolvent content
3.0359.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.116α = 90
b = 75.117β = 90
c = 107.192γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMULTILAYER2008-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R

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
11.7133.0897.90.0714.42.443966
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)
11.711.896.20.244.72.5

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 2V231.7130.7741470222297.40.17840.176670.20878RANDOM17.13
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.365
r_dihedral_angle_4_deg24.77
r_dihedral_angle_3_deg13.711
r_dihedral_angle_1_deg5.702
r_scangle_it2.737
r_scbond_it1.796
r_angle_refined_deg1.28
r_mcangle_it1.069
r_mcbond_it0.7
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.365
r_dihedral_angle_4_deg24.77
r_dihedral_angle_3_deg13.711
r_dihedral_angle_1_deg5.702
r_scangle_it2.737
r_scbond_it1.796
r_angle_refined_deg1.28
r_mcangle_it1.069
r_mcbond_it0.7
r_nbtor_refined0.309
r_nbd_refined0.21
r_xyhbond_nbd_refined0.117
r_chiral_restr0.107
r_bond_refined_d0.012
r_gen_planes_refined0.005
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_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms2371
Nucleic Acid Atoms
Solvent Atoms577
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling