3LP3

p15 HIV RNaseH domain with inhibitor MK3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop6.82980.1 M Sodium citrate pH 5.0, 15-20% PEG 8000, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8256.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.256α = 90
b = 51.256β = 90
c = 112.773γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSaturn 944+SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54

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
12.8501000.098105.88172
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)
2.82.91000.3595.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.834.88775138799.890.232270.229470.28828RANDOM37.307
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]
-0.17-0.08-0.170.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.386
r_dihedral_angle_3_deg17.695
r_dihedral_angle_4_deg9.577
r_dihedral_angle_1_deg4.764
r_angle_refined_deg1.029
r_scangle_it0.764
r_mcangle_it0.693
r_scbond_it0.427
r_mcbond_it0.379
r_nbtor_refined0.292
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.386
r_dihedral_angle_3_deg17.695
r_dihedral_angle_4_deg9.577
r_dihedral_angle_1_deg4.764
r_angle_refined_deg1.029
r_scangle_it0.764
r_mcangle_it0.693
r_scbond_it0.427
r_mcbond_it0.379
r_nbtor_refined0.292
r_symmetry_vdw_refined0.184
r_nbd_refined0.183
r_symmetry_hbond_refined0.116
r_xyhbond_nbd_refined0.1
r_chiral_restr0.064
r_metal_ion_refined0.019
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2020
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms64

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction