X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DV2PDB ENTRY 1DV2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M KCL, 3-8% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.7855.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.129α = 90
b = 106.784β = 90
c = 121.91γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002007-05-07MSINGLE 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
12.620960.117.833.832843
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)
12.62.6996.70.543.33.8

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 1DV22.62031155166895.50.1920.1890.247RANDOM38.83
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]
-0.962.37-1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.653
r_dihedral_angle_4_deg17.388
r_dihedral_angle_3_deg15.294
r_dihedral_angle_1_deg5.334
r_scangle_it1.391
r_angle_refined_deg1.111
r_scbond_it0.895
r_angle_other_deg0.741
r_mcangle_it0.565
r_mcbond_it0.509
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.653
r_dihedral_angle_4_deg17.388
r_dihedral_angle_3_deg15.294
r_dihedral_angle_1_deg5.334
r_scangle_it1.391
r_angle_refined_deg1.111
r_scbond_it0.895
r_angle_other_deg0.741
r_mcangle_it0.565
r_mcbond_it0.509
r_nbd_refined0.19
r_nbd_other0.172
r_nbtor_refined0.172
r_symmetry_vdw_other0.163
r_xyhbond_nbd_refined0.138
r_symmetry_vdw_refined0.122
r_nbtor_other0.078
r_symmetry_hbond_refined0.074
r_chiral_restr0.062
r_bond_refined_d0.009
r_bond_other_d0.003
r_gen_planes_refined0.003
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 Atoms6755
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata reduction
SCALEPACKdata scaling
MOLREPphasing