2O40

Crystal Structure of a Chemically Synthesized 203 Amino Acid 'Covalent Dimer' HIV-1 Protease Molecule


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62930.1M citrate, 0.2M sodium phophate, 30% (w/v) ammonium sulfate, 10% (v/v) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0439.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.326α = 90
b = 58.306β = 90
c = 61.699γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCH2006-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.97932APS23-ID-B

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
11.655098.30.07214.64.8227282234216721672
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)
11.6511.69488.680.7492.674.61583

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.65202166521383116398.70.193350.191060.23748RANDOM19.973
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]
0.06-0.150.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.376
r_dihedral_angle_4_deg17.352
r_dihedral_angle_3_deg13.449
r_dihedral_angle_1_deg6.214
r_scangle_it4.005
r_scbond_it2.626
r_mcangle_it1.811
r_angle_refined_deg1.599
r_mcbond_it1.168
r_angle_other_deg0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.376
r_dihedral_angle_4_deg17.352
r_dihedral_angle_3_deg13.449
r_dihedral_angle_1_deg6.214
r_scangle_it4.005
r_scbond_it2.626
r_mcangle_it1.811
r_angle_refined_deg1.599
r_mcbond_it1.168
r_angle_other_deg0.89
r_mcbond_other0.339
r_symmetry_hbond_refined0.297
r_nbd_refined0.205
r_nbd_other0.194
r_symmetry_vdw_refined0.188
r_nbtor_refined0.169
r_symmetry_vdw_other0.167
r_xyhbond_nbd_refined0.108
r_chiral_restr0.105
r_nbtor_other0.091
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1543
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms54

Software

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