5VAJ | pdb_00005vaj

BhRNase H - amide-RNA/DNA complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZBI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529150 mM sodium cacodylate (pH 6.5) and 0.7 M sodium acetate.
Crystal Properties
Matthews coefficientSolvent content
2.5652.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.18α = 90
b = 37.513β = 121.65
c = 93.863γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2016-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.958099.90.0918.475.130154
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)
11.952.0299.60.464.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1ZBI1.9579.928679147299.80.168130.165640.170.216940.22RANDOM23.188
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]
-0.23-0.450.760.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.34
r_dihedral_angle_4_deg18.827
r_dihedral_angle_3_deg16.024
r_dihedral_angle_1_deg7.301
r_long_range_B_refined6.585
r_long_range_B_other6.483
r_scangle_other4.664
r_mcangle_other3.262
r_mcangle_it3.258
r_scbond_it3.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.34
r_dihedral_angle_4_deg18.827
r_dihedral_angle_3_deg16.024
r_dihedral_angle_1_deg7.301
r_long_range_B_refined6.585
r_long_range_B_other6.483
r_scangle_other4.664
r_mcangle_other3.262
r_mcangle_it3.258
r_scbond_it3.014
r_scbond_other3.013
r_mcbond_it2.258
r_mcbond_other2.223
r_angle_other_deg1.905
r_angle_refined_deg1.38
r_chiral_restr0.15
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2182
Nucleic Acid Atoms494
Solvent Atoms214
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing