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
2.6954.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.509α = 90
b = 78.919β = 90
c = 129.128γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray130IMAGE PLATERIGAKU RAXIS IV++osmic2004-08-20MSINGLE 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
12.52097.50.07320.52563724997-1-1
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)
12.52.5995.40.4032.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1R1W2.52024997130597.60.240610.240610.237880.29414RANDOM51.24
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]
4.68-3.39-1.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.518
r_dihedral_angle_3_deg17.748
r_dihedral_angle_4_deg17.166
r_dihedral_angle_1_deg5.352
r_scangle_it1.369
r_angle_refined_deg1.254
r_scbond_it0.856
r_mcangle_it0.751
r_mcbond_it0.423
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.518
r_dihedral_angle_3_deg17.748
r_dihedral_angle_4_deg17.166
r_dihedral_angle_1_deg5.352
r_scangle_it1.369
r_angle_refined_deg1.254
r_scbond_it0.856
r_mcangle_it0.751
r_mcbond_it0.423
r_nbtor_refined0.312
r_nbd_refined0.204
r_symmetry_vdw_refined0.195
r_xyhbond_nbd_refined0.154
r_symmetry_hbond_refined0.096
r_chiral_restr0.089
r_bond_refined_d0.009
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4233
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing