X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B7WPDB ENTRY 3B7W

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2M AMMONIUM ACETATE, 0.1M TRIS PH 8.5, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4249.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.73α = 90
b = 97.73β = 90
c = 384.6γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100RIGAKU AREA DETECTOROSMIC2008-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT

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
12.4537.9998.10.019.583734022
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)
12.452.7197.10.4923

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 3B7W2.4539.166561234541000.1960.1930.243RANDOM1.86
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]
-0.04-0.040.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.146
r_dihedral_angle_4_deg15.28
r_dihedral_angle_3_deg14.966
r_dihedral_angle_1_deg5.821
r_scangle_it2.581
r_scbond_it1.951
r_angle_refined_deg1.452
r_angle_other_deg0.919
r_mcangle_it0.596
r_mcbond_it0.381
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.146
r_dihedral_angle_4_deg15.28
r_dihedral_angle_3_deg14.966
r_dihedral_angle_1_deg5.821
r_scangle_it2.581
r_scbond_it1.951
r_angle_refined_deg1.452
r_angle_other_deg0.919
r_mcangle_it0.596
r_mcbond_it0.381
r_symmetry_hbond_refined0.217
r_symmetry_vdw_refined0.215
r_nbd_refined0.21
r_nbd_other0.198
r_symmetry_vdw_other0.194
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.179
r_chiral_restr0.112
r_nbtor_other0.085
r_bond_refined_d0.013
r_gen_planes_refined0.004
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 Atoms12382
Nucleic Acid Atoms
Solvent Atoms655
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing