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 17 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 30% MPD, 0.1 M CITRATE PH 7.5, 0.2 M MGACETATE. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 1 MM MNCL2 FOR 45 MIN AT 4C PRIOR TO CRYOCOOLING.
Crystal Properties
Matthews coefficientSolvent content
5.677.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.578α = 90
b = 138.578β = 90
c = 231.389γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRRORS2005-05-31MSINGLE 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
12.46094.10.1113.95.941368640.42
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)
12.42.5391.30.552.54.5

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 ENTRY 2BHC2.4119.5239342202693.50.1740.1720.207RANDOM38.44
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]
1.091.09-2.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.002
r_dihedral_angle_4_deg15.65
r_dihedral_angle_3_deg12.88
r_dihedral_angle_1_deg5.909
r_scangle_it2.985
r_scbond_it1.887
r_mcangle_it1.219
r_angle_refined_deg1.178
r_mcbond_it0.819
r_angle_other_deg0.755
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.002
r_dihedral_angle_4_deg15.65
r_dihedral_angle_3_deg12.88
r_dihedral_angle_1_deg5.909
r_scangle_it2.985
r_scbond_it1.887
r_mcangle_it1.219
r_angle_refined_deg1.178
r_mcbond_it0.819
r_angle_other_deg0.755
r_symmetry_vdw_other0.255
r_symmetry_vdw_refined0.244
r_nbd_refined0.195
r_nbtor_refined0.172
r_nbd_other0.17
r_symmetry_hbond_refined0.138
r_xyhbond_nbd_refined0.13
r_nbtor_other0.08
r_chiral_restr0.064
r_bond_refined_d0.01
r_gen_planes_refined0.003
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 Atoms3483
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling