X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RRFPDB entry 1RRF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6291PEG 4000, ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.657α = 112.96
b = 48.775β = 97.69
c = 55.905γ = 90
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVCONFOCAL MAXFLUX2005-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.5418

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
12.450.90.04810.91.9139171391711
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)
2.42.49950.08751.9

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1RRF2.450.9139171321470295.730.23550.233070.28277RANDOM25.023
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]
-1.010.310.07-1.491.833.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.843
r_dihedral_angle_4_deg18.245
r_dihedral_angle_3_deg16.588
r_dihedral_angle_1_deg4.777
r_scangle_it3.971
r_scbond_it2.496
r_mcangle_it1.749
r_angle_refined_deg1.704
r_mcbond_it0.943
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.843
r_dihedral_angle_4_deg18.245
r_dihedral_angle_3_deg16.588
r_dihedral_angle_1_deg4.777
r_scangle_it3.971
r_scbond_it2.496
r_mcangle_it1.749
r_angle_refined_deg1.704
r_mcbond_it0.943
r_nbtor_refined0.308
r_symmetry_vdw_refined0.259
r_nbd_refined0.247
r_symmetry_hbond_refined0.164
r_xyhbond_nbd_refined0.158
r_chiral_restr0.106
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2740
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing