X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YDSPDB ENTRY 1YDS

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.3948.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.809α = 90
b = 74.788β = 90
c = 80.363γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
12.0835940.0510.82.324115
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)
12.0835870.233.12.2

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 1YDS2.0835.424115127393.60.210.2060.276RANDOM21.7
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]
0.160.78-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.676
r_dihedral_angle_4_deg17.718
r_dihedral_angle_3_deg16.027
r_dihedral_angle_1_deg6.173
r_angle_refined_deg1.505
r_angle_other_deg0.953
r_symmetry_vdw_other0.355
r_nbd_refined0.201
r_nbd_other0.193
r_nbtor_refined0.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.676
r_dihedral_angle_4_deg17.718
r_dihedral_angle_3_deg16.027
r_dihedral_angle_1_deg6.173
r_angle_refined_deg1.505
r_angle_other_deg0.953
r_symmetry_vdw_other0.355
r_nbd_refined0.201
r_nbd_other0.193
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.152
r_symmetry_hbond_refined0.148
r_symmetry_vdw_refined0.146
r_scangle_it0.132
r_scbond_it0.113
r_mcangle_it0.109
r_chiral_restr0.093
r_nbtor_other0.086
r_mcbond_it0.086
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_other
r_scbond_other
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 Atoms2935
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement