X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BVAPDB ENTRIES 2BVA, 1YHW, 1YHV, 1F3M
experimental modelPDB 1YHWPDB ENTRIES 2BVA, 1YHW, 1YHV, 1F3M
experimental modelPDB 1YHVPDB ENTRIES 2BVA, 1YHW, 1YHV, 1F3M
experimental modelPDB 1F3MPDB ENTRIES 2BVA, 1YHW, 1YHV, 1F3M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.51.60M MGSO4 0.1M MES PH 6.5 SITTING DROPS, 150NL AND 50NL PROTEIN AND RESERVOIR MIX.
Crystal Properties
Matthews coefficientSolvent content
2.5751.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.781α = 90
b = 66.674β = 90
c = 96.999γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHDYNAMICALLY BENDABLE MIRROR2005-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.65598.80.0811.13.5177870-3
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)
11.61.6993.60.572.12.5

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 ENTRIES 2BVA, 1YHW, 1YHV, 1F3M1.654.9649551167598.60.1980.1970.222RANDOM21.82
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]
0.48-0.28-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.029
r_dihedral_angle_4_deg20.083
r_dihedral_angle_3_deg13.074
r_dihedral_angle_1_deg6.096
r_scangle_it3.905
r_scbond_it2.531
r_angle_refined_deg1.61
r_mcangle_it1.601
r_mcbond_it1.221
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.029
r_dihedral_angle_4_deg20.083
r_dihedral_angle_3_deg13.074
r_dihedral_angle_1_deg6.096
r_scangle_it3.905
r_scbond_it2.531
r_angle_refined_deg1.61
r_mcangle_it1.601
r_mcbond_it1.221
r_nbtor_refined0.31
r_nbtor_other0.272
r_nbd_refined0.212
r_symmetry_vdw_refined0.183
r_xyhbond_nbd_refined0.159
r_symmetry_hbond_refined0.131
r_chiral_restr0.119
r_angle_other_deg0.046
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_nbd_other0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms2288
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing