X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VWUPDB ENTRY 2VWU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5291PROTEIN: 12MG/ML IN 50MM MOPS PH 6.5, 50MM NACL, 1MM DTT RESERVOIR: 25% PEG 5000 MME, 0.1M TRIS PH 7.5, 0.15M MGCL2, 15% GLYCEROL TEMP: 18 DEGREES C SITTING DROP: 2 UL PROTEIN, 0.6 UL RESERVOIR
Crystal Properties
Matthews coefficientSolvent content
2.1442.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.123α = 90
b = 53.492β = 110.91
c = 61.265γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU-MSCMIRRORS2005-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
12.11001000.135.63.66164262
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)
12.12.181000.312.83.6

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 2VWU2.157.261559583199.950.186810.184360.23286RANDOM22.306
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]
0.35-0.58-1.070.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.595
r_dihedral_angle_4_deg15.006
r_dihedral_angle_3_deg13.485
r_dihedral_angle_1_deg5.953
r_scangle_it2.785
r_scbond_it1.863
r_angle_refined_deg1.461
r_mcangle_it1.258
r_mcbond_it0.872
r_angle_other_deg0.819
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.595
r_dihedral_angle_4_deg15.006
r_dihedral_angle_3_deg13.485
r_dihedral_angle_1_deg5.953
r_scangle_it2.785
r_scbond_it1.863
r_angle_refined_deg1.461
r_mcangle_it1.258
r_mcbond_it0.872
r_angle_other_deg0.819
r_symmetry_vdw_other0.246
r_symmetry_hbond_refined0.237
r_nbd_refined0.218
r_nbtor_refined0.189
r_xyhbond_nbd_refined0.183
r_nbd_other0.177
r_symmetry_vdw_refined0.115
r_chiral_restr0.088
r_nbtor_other0.081
r_bond_refined_d0.013
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 Atoms2109
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing