X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z83PDB ENTRY 1Z83

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
173.4 M NAMALONATE 1 MM ZNSO4, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
2.244.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.535α = 90
b = 69.998β = 90
c = 88.558γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATE2005-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E

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
11.7132.5588.50.0914.515.337771
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)
11.711.8141.30.224.060.93

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 1Z831.715035815189188.60.1780.1760.228RANDOM4.87
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]
-0.430.71-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.526
r_dihedral_angle_3_deg13.692
r_dihedral_angle_4_deg12.573
r_dihedral_angle_1_deg5.767
r_scangle_it5.478
r_scbond_it4.047
r_mcangle_it2.184
r_mcbond_it1.656
r_angle_refined_deg1.593
r_angle_other_deg0.995
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.526
r_dihedral_angle_3_deg13.692
r_dihedral_angle_4_deg12.573
r_dihedral_angle_1_deg5.767
r_scangle_it5.478
r_scbond_it4.047
r_mcangle_it2.184
r_mcbond_it1.656
r_angle_refined_deg1.593
r_angle_other_deg0.995
r_symmetry_vdw_other0.325
r_nbd_refined0.215
r_nbd_other0.197
r_symmetry_vdw_refined0.176
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.163
r_symmetry_hbond_refined0.132
r_nbtor_other0.084
r_chiral_restr0.083
r_bond_refined_d0.015
r_gen_planes_refined0.006
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 Atoms2983
Nucleic Acid Atoms
Solvent Atoms380
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing