X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QJAPDB ENTRY 1QJA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.2M SODIUM ACETATE TRIHYDRATE, 0.1M TRISHCL PH8.5,30% PEG4000, pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.307α = 90
b = 85.964β = 112.67
c = 64.666γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU-MSC R-AXIS HTCOSMIC MIRRORS2005-05-21MSINGLE 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
12.834.8896.40.0917.76.314743
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)
12.82.9593.30.413.55.8

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 1QJA2.859.6613606112195.90.210.2060.259RANDOM51.8
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]
-3.01-0.453.62-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.099
r_dihedral_angle_3_deg16.878
r_dihedral_angle_4_deg14.445
r_dihedral_angle_1_deg6.332
r_scangle_it2.106
r_angle_refined_deg1.404
r_scbond_it1.31
r_angle_other_deg0.839
r_mcangle_it0.836
r_mcbond_it0.541
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.099
r_dihedral_angle_3_deg16.878
r_dihedral_angle_4_deg14.445
r_dihedral_angle_1_deg6.332
r_scangle_it2.106
r_angle_refined_deg1.404
r_scbond_it1.31
r_angle_other_deg0.839
r_mcangle_it0.836
r_mcbond_it0.541
r_symmetry_vdw_other0.288
r_nbd_refined0.252
r_symmetry_vdw_refined0.238
r_symmetry_hbond_refined0.202
r_nbtor_refined0.195
r_nbd_other0.172
r_xyhbond_nbd_refined0.144
r_nbtor_other0.093
r_chiral_restr0.078
r_bond_refined_d0.015
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3727
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing