X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BHCPDB ENTRY 2BHC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277SITTING DROP VAPOUR DIFFUSION AT 4C. 2 UL 7 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 28% MPD, 0.1 M CITRATE PH 7.5, 0.2 M MGACETATE. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 1 MM MNCL2 FOR 30 MIN AT 4C PRIOR TO CRYOCOOLING.
Crystal Properties
Matthews coefficientSolvent content
5.677.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.17α = 90
b = 138.17β = 90
c = 231.296γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRRORS2005-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200H

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
12.674.5497.20.11145.433663658.02
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)
12.62.7486.60.592.44.6

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 2BHC2.6169.6732029163098.40.1740.1720.204RANDOM44.33
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]
1.331.33-2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.004
r_dihedral_angle_4_deg17.661
r_dihedral_angle_3_deg13.805
r_dihedral_angle_1_deg5.898
r_scangle_it2.662
r_scbond_it1.66
r_angle_refined_deg1.181
r_mcangle_it1.147
r_mcbond_it0.756
r_angle_other_deg0.754
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.004
r_dihedral_angle_4_deg17.661
r_dihedral_angle_3_deg13.805
r_dihedral_angle_1_deg5.898
r_scangle_it2.662
r_scbond_it1.66
r_angle_refined_deg1.181
r_mcangle_it1.147
r_mcbond_it0.756
r_angle_other_deg0.754
r_symmetry_vdw_refined0.305
r_symmetry_vdw_other0.284
r_nbd_refined0.207
r_nbtor_refined0.178
r_nbd_other0.17
r_xyhbond_nbd_refined0.132
r_symmetry_hbond_refined0.107
r_nbtor_other0.08
r_chiral_restr0.065
r_bond_refined_d0.01
r_gen_planes_refined0.004
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 Atoms3484
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling