X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R1WPDB entry 1r1w

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION529812% PEG 6000, 1.0M LiCl2, 0.1M Sodium Citrate, pH 5.0, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7355.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.205α = 90
b = 78.25β = 90
c = 129.684γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray130IMAGE PLATERIGAKU RAXIS IV++osmic2004-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

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
12.219.6497.80.057203.64021739332-3-3
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)
2.22.2893.90.4222.53699

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1r1w2.219.643808737276196797.870.257460.257460.255650.29185RANDOM38.372
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]
2.33-1.59-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.528
r_dihedral_angle_3_deg15.583
r_dihedral_angle_4_deg13.805
r_dihedral_angle_1_deg4.773
r_scangle_it1.493
r_angle_refined_deg1.096
r_scbond_it0.924
r_mcangle_it0.915
r_mcbond_it0.51
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.528
r_dihedral_angle_3_deg15.583
r_dihedral_angle_4_deg13.805
r_dihedral_angle_1_deg4.773
r_scangle_it1.493
r_angle_refined_deg1.096
r_scbond_it0.924
r_mcangle_it0.915
r_mcbond_it0.51
r_nbtor_refined0.303
r_nbd_refined0.187
r_symmetry_vdw_refined0.18
r_symmetry_hbond_refined0.145
r_xyhbond_nbd_refined0.132
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4299
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms76

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling