3QIN

Crystal Structure of HIV-1 RNase H p15 with engineered E. coli loop and pyrimidinol carboxylic acid inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HRHPDB ENTRY 1HRH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52931.8M (NH4)2SO4, 100mM HEPES pH 7.5, and 3% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.957.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.841α = 90
b = 90.37β = 90
c = 111.922γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2006-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54

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
11.696750970.05110.63.121540
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)
11.69671.73950.333.12.9

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 1HRH1.696723.11820866193293.640.22330.22030.253random
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]
13.2293-8.2099-5.0194
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.902
f_angle_d1.137
f_chiral_restr0.11
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1082
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms28

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling