X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XS1PDB ENTRY 1XS1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298PEG 400, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.141

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 179.93α = 90
b = 63.073β = 102.18
c = 96.363γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMARRESEARCH2004-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
122597.40.10883.97184371843
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0595.50.4542.6

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 1XS122566024352797.140.260880.258090.31288RANDOM19.091
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]
-0.910.640.190.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.204
r_dihedral_angle_4_deg21.194
r_dihedral_angle_3_deg15.705
r_dihedral_angle_1_deg7.131
r_scangle_it2.544
r_scbond_it1.702
r_angle_refined_deg1.593
r_mcangle_it1.147
r_angle_other_deg0.903
r_mcbond_it0.791
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.204
r_dihedral_angle_4_deg21.194
r_dihedral_angle_3_deg15.705
r_dihedral_angle_1_deg7.131
r_scangle_it2.544
r_scbond_it1.702
r_angle_refined_deg1.593
r_mcangle_it1.147
r_angle_other_deg0.903
r_mcbond_it0.791
r_symmetry_hbond_refined0.261
r_symmetry_vdw_refined0.224
r_symmetry_vdw_other0.223
r_nbd_refined0.2
r_nbd_other0.192
r_mcbond_other0.19
r_xyhbond_nbd_refined0.185
r_xyhbond_nbd_other0.18
r_metal_ion_refined0.121
r_chiral_restr0.089
r_nbtor_other0.084
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8952
Nucleic Acid Atoms
Solvent Atoms391
Heterogen Atoms175

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing