X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VYOPDB ENTRY 1VYO

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.8857.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.669α = 90
b = 99.936β = 90
c = 135.191γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.42599.60.07146257876-3
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)
11.41.5990.5535.9

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 1VYO1.481.652449721289499.50.1750.1740.201RANDOM14.46
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]
-0.480.110.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.793
r_dihedral_angle_4_deg22.043
r_dihedral_angle_3_deg11.874
r_dihedral_angle_1_deg7.139
r_scangle_it3.508
r_scbond_it2.402
r_angle_refined_deg1.697
r_mcangle_it1.639
r_mcbond_it1.36
r_angle_other_deg0.869
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.793
r_dihedral_angle_4_deg22.043
r_dihedral_angle_3_deg11.874
r_dihedral_angle_1_deg7.139
r_scangle_it3.508
r_scbond_it2.402
r_angle_refined_deg1.697
r_mcangle_it1.639
r_mcbond_it1.36
r_angle_other_deg0.869
r_symmetry_vdw_other0.254
r_symmetry_hbond_refined0.222
r_nbd_other0.202
r_symmetry_vdw_refined0.197
r_nbd_refined0.191
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.161
r_chiral_restr0.108
r_nbtor_other0.086
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms7573
Nucleic Acid Atoms
Solvent Atoms1168
Heterogen Atoms234

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing