X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RY9PDB ENTRY 1RY9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16100 MM GUANIDINIUM CHLORIDE, 100 MM MES PH 6.0, 50 MM AMMONIUM SULPHATE, 5% ETHYLENE GLYCOL
Crystal Properties
Matthews coefficientSolvent content
2.0941

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.98α = 90
b = 50.38β = 117.03
c = 57.68γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC QUANTUM 315KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING2009-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
1251.3898.70.174.43.51926617.9
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)
122.1198.70.7323.5

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 1RY92.351.381203665098.280.225740.223690.26375RANDOM21.956
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]
0.780.53-1.240.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.095
r_dihedral_angle_4_deg15.338
r_dihedral_angle_3_deg12.971
r_dihedral_angle_1_deg6.99
r_angle_refined_deg1.284
r_angle_other_deg0.896
r_symmetry_vdw_other0.281
r_symmetry_vdw_refined0.213
r_symmetry_hbond_refined0.208
r_xyhbond_nbd_refined0.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.095
r_dihedral_angle_4_deg15.338
r_dihedral_angle_3_deg12.971
r_dihedral_angle_1_deg6.99
r_angle_refined_deg1.284
r_angle_other_deg0.896
r_symmetry_vdw_other0.281
r_symmetry_vdw_refined0.213
r_symmetry_hbond_refined0.208
r_xyhbond_nbd_refined0.159
r_chiral_restr0.07
r_mcbond_it0.012
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
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_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms2038
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing